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This page was generated on 2023-06-06 11:00:27 -0000 (Tue, 06 Jun 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.0 (2023-04-21) -- "Already Tomorrow" 4366
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CHECK results for biodbLipidmaps on kunpeng2


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.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 195/2199HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbLipidmaps 1.7.0  (landing page)
Pierrick Roger
Snapshot Date: 2023-06-05 06:35:06 -0000 (Mon, 05 Jun 2023)
git_url: https://git.bioconductor.org/packages/biodbLipidmaps
git_branch: devel
git_last_commit: 0466597
git_last_commit_date: 2023-04-25 15:34:40 -0000 (Tue, 25 Apr 2023)
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

Summary

Package: biodbLipidmaps
Version: 1.7.0
Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings biodbLipidmaps_1.7.0.tar.gz
StartedAt: 2023-06-05 18:16:46 -0000 (Mon, 05 Jun 2023)
EndedAt: 2023-06-05 18:22:34 -0000 (Mon, 05 Jun 2023)
EllapsedTime: 348.5 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbLipidmaps.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings biodbLipidmaps_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/biodbLipidmaps.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘biodbLipidmaps/DESCRIPTION’ ... OK
* this is package ‘biodbLipidmaps’ version ‘1.7.0’
* 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 R 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 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’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘biodbLipidmaps.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

biodbLipidmaps.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL biodbLipidmaps
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.0/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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbLipidmaps)

Tests output

biodbLipidmaps.Rcheck/tests/testthat.Rout


R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbLipidmaps")
biodb.INFO [2023-06-05 18:17:59.261][biodb::testContext]
biodb.INFO [2023-06-05 18:17:59.264][biodb::testContext] ********************************************************************************
biodb.INFO [2023-06-05 18:17:59.265][biodb::testContext] Test context - Generic tests
biodb.INFO [2023-06-05 18:17:59.267][biodb::testContext] ********************************************************************************
biodb.INFO [2023-06-05 18:17:59.268][biodb::testContext]
biodb.INFO [2023-06-05 18:17:59.288][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.9.0.
biodb.DEBUG[2023-06-05 18:17:59.290][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.0/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-06-05 18:17:59.299][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-06-05 18:17:59.301][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-06-05 18:17:59.302][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-06-05 18:17:59.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:59.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:59.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:59.308][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-06-05 18:17:59.336][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-06-05 18:17:59.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:59.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:59.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:59.341][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-06-05 18:17:59.343][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-06-05 18:17:59.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:59.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:59.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:59.348][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-06-05 18:17:59.350][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-06-05 18:17:59.351][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-06-05 18:17:59.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:59.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:59.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:59.357][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-06-05 18:17:59.358][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-06-05 18:17:59.360][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-06-05 18:17:59.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:59.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:59.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:59.366][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-06-05 18:17:59.367][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-06-05 18:17:59.368][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:59.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:59.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:59.373][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-06-05 18:17:59.374][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-06-05 18:17:59.376][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-06-05 18:17:59.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:59.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:59.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:59.381][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-06-05 18:17:59.383][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-06-05 18:17:59.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:59.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:59.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:59.388][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-06-05 18:17:59.390][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-06-05 18:17:59.391][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-06-05 18:17:59.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:59.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:59.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:59.397][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-06-05 18:17:59.398][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-06-05 18:17:59.400][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-06-05 18:17:59.402][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-06-05 18:17:59.403][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-06-05 18:17:59.405][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-06-05 18:17:59.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:59.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:59.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:59.410][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-06-05 18:17:59.412][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-06-05 18:17:59.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:59.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:59.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:59.417][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-06-05 18:17:59.419][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-06-05 18:17:59.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:59.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:59.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:59.424][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-06-05 18:17:59.426][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-06-05 18:17:59.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:59.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:59.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:59.432][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-06-05 18:17:59.433][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-06-05 18:17:59.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:59.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:59.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:59.439][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-06-05 18:17:59.440][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-06-05 18:17:59.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:59.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:59.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:59.446][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-06-05 18:17:59.447][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-06-05 18:17:59.452][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-06-05 18:17:59.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:59.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:59.456][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[2023-06-05 18:17:59.458][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-06-05 18:17:59.459][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-06-05 18:17:59.461][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-06-05 18:17:59.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:59.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:59.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:59.470][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-06-05 18:17:59.518][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:59.552][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-06-05 18:17:59.554][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:59.555][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-06-05 18:17:59.557][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:59.558][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-06-05 18:17:59.560][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:59.561][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-06-05 18:17:59.562][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-06-05 18:17:59.564][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-06-05 18:17:59.565][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:59.567][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-06-05 18:17:59.568][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-06-05 18:17:59.569][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:59.571][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:59.572][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-06-05 18:17:59.572][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-06-05 18:17:59.572][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-06-05 18:17:59.572][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-06-05 18:17:59.572][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-06-05 18:17:59.574][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-06-05 18:17:59.575][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:17:59.576][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:17:59.578][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-06-05 18:17:59.579][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:17:59.580][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:17:59.581][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-06-05 18:17:59.583][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:59.584][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-06-05 18:17:59.585][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-06-05 18:17:59.587][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:59.588][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:59.590][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-06-05 18:17:59.592][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:59.594][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-06-05 18:17:59.595][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:59.597][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-06-05 18:17:59.598][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:59.600][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-06-05 18:17:59.601][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:59.602][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-06-05 18:17:59.604][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-06-05 18:17:59.605][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-06-05 18:17:59.607][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:59.608][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-06-05 18:17:59.610][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-06-05 18:17:59.611][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:59.612][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:59.614][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-06-05 18:17:59.614][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-06-05 18:17:59.614][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-06-05 18:17:59.614][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-06-05 18:17:59.614][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-06-05 18:17:59.615][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-06-05 18:17:59.617][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:17:59.618][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:17:59.620][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-06-05 18:17:59.621][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:17:59.622][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:17:59.624][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-06-05 18:17:59.625][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:59.627][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-06-05 18:17:59.628][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-06-05 18:17:59.629][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:59.631][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:59.632][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-06-05 18:17:59.635][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:59.636][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-06-05 18:17:59.638][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:59.639][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-06-05 18:17:59.641][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:59.642][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-06-05 18:17:59.643][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:59.645][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-06-05 18:17:59.646][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-06-05 18:17:59.648][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-06-05 18:17:59.649][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:59.651][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-06-05 18:17:59.652][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-06-05 18:17:59.653][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:59.655][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:59.656][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:59.658][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-06-05 18:17:59.659][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:17:59.660][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:17:59.662][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-06-05 18:17:59.663][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:17:59.664][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:17:59.666][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-06-05 18:17:59.667][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:59.669][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-06-05 18:17:59.670][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-06-05 18:17:59.671][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:59.673][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:59.674][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-06-05 18:17:59.677][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:59.678][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-06-05 18:17:59.680][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:59.681][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-06-05 18:17:59.683][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:59.684][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-06-05 18:17:59.685][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:59.687][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-06-05 18:17:59.688][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-06-05 18:17:59.690][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-06-05 18:17:59.691][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:59.693][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-06-05 18:17:59.694][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-06-05 18:17:59.695][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:59.697][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-06-05 18:17:59.698][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:59.700][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-06-05 18:17:59.701][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:17:59.702][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:17:59.704][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-06-05 18:17:59.705][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:17:59.707][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:17:59.708][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-06-05 18:17:59.709][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:59.711][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-06-05 18:17:59.712][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-06-05 18:17:59.713][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-06-05 18:17:59.715][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:17:59.720][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-06-05 18:17:59.721][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:59.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:59.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:59.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:59.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:59.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:59.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:59.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:59.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:59.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:59.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:59.735][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[2023-06-05 18:17:59.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:59.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:59.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:59.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:59.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:59.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:59.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:59.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:59.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:59.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:59.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:59.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:59.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:59.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:59.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:59.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:59.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:59.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:59.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:59.761][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[2023-06-05 18:17:59.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:59.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:59.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:59.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:59.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:59.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:59.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:59.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:59.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:59.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:59.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:59.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:59.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:59.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:59.780][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[2023-06-05 18:17:59.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:59.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:59.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:59.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:59.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:59.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:59.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:59.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:59.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:59.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:59.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:59.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:59.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:59.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:59.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:59.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:59.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:59.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:59.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:59.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:59.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:59.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:59.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:59.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:59.812][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[2023-06-05 18:17:59.813][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:59.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:59.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:59.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:59.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:59.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:59.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:59.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:59.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:59.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:59.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:17:59.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:17:59.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:17:59.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:17:59.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:17:59.833][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-06-05 18:17:59.839][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-06-05 18:17:59.841][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-06-05 18:17:59.843][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-06-05 18:17:59.845][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-06-05 18:17:59.847][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-06-05 18:17:59.849][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-06-05 18:17:59.851][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-06-05 18:17:59.853][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-06-05 18:17:59.855][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-06-05 18:17:59.857][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-06-05 18:17:59.859][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-06-05 18:17:59.861][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-06-05 18:17:59.863][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-06-05 18:17:59.865][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-06-05 18:17:59.867][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-06-05 18:17:59.869][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-06-05 18:17:59.871][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-06-05 18:17:59.873][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-06-05 18:17:59.875][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-06-05 18:17:59.877][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-06-05 18:17:59.879][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-06-05 18:17:59.881][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-06-05 18:17:59.884][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-06-05 18:17:59.886][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-06-05 18:17:59.888][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-06-05 18:17:59.890][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-06-05 18:17:59.892][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-06-05 18:17:59.894][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-06-05 18:17:59.896][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-06-05 18:17:59.898][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-06-05 18:17:59.907][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-06-05 18:17:59.909][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-06-05 18:17:59.911][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-06-05 18:17:59.913][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-06-05 18:17:59.915][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-06-05 18:17:59.917][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-06-05 18:17:59.919][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-06-05 18:17:59.921][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-06-05 18:17:59.923][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-06-05 18:17:59.925][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-06-05 18:17:59.928][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-06-05 18:17:59.930][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-06-05 18:17:59.932][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-06-05 18:17:59.934][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-06-05 18:17:59.936][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-06-05 18:17:59.938][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-06-05 18:17:59.940][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-06-05 18:17:59.942][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-06-05 18:17:59.944][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-06-05 18:17:59.946][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-06-05 18:17:59.948][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-06-05 18:17:59.950][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-06-05 18:17:59.952][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-06-05 18:17:59.954][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-06-05 18:17:59.956][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-06-05 18:17:59.959][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-06-05 18:17:59.961][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-06-05 18:17:59.963][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-06-05 18:17:59.965][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-06-05 18:17:59.967][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-06-05 18:17:59.969][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-06-05 18:17:59.971][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-06-05 18:17:59.973][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-06-05 18:17:59.975][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-06-05 18:17:59.977][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-06-05 18:17:59.979][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-06-05 18:17:59.981][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-06-05 18:17:59.983][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-06-05 18:17:59.986][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-06-05 18:17:59.988][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-06-05 18:17:59.990][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-06-05 18:17:59.992][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-06-05 18:17:59.994][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-06-05 18:17:59.996][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-06-05 18:17:59.998][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-06-05 18:18:00.000][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-06-05 18:18:00.002][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-06-05 18:18:00.004][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-06-05 18:18:00.006][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-06-05 18:18:00.008][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-06-05 18:18:00.010][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-06-05 18:18:00.012][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-06-05 18:18:00.021][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-06-05 18:18:00.023][initialize] This is biodb version 1.9.0.
biodb.DEBUG[2023-06-05 18:18:00.027][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-06-05 18:18:00.028][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:18:00.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:18:00.031][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:18:00.032][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[2023-06-05 18:18:00.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:18:00.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:18:00.041][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:18:00.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:18:00.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:18:00.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:18:00.046][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[2023-06-05 18:18:00.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:18:00.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:18:00.050][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:18:00.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:18:00.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:18:00.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:18:00.055][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[2023-06-05 18:18:00.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:18:00.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:18:00.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:18:00.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:18:00.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:18:00.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:18:00.064][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[2023-06-05 18:18:00.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:18:00.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:18:00.068][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:18:00.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:18:00.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:18:00.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:18:00.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:18:00.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:18:00.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:18:00.077][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:18:00.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:18:00.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:18:00.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:18:00.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:18:00.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:18:00.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:18:00.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:18:00.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:18:00.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:18:00.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:18:00.091][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[2023-06-05 18:18:00.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:18:00.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:18:00.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:18:00.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:18:00.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:18:00.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:18:00.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:18:00.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:18:00.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:18:00.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:18:00.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:18:00.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:18:00.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:18:00.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:18:00.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:18:00.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:18:00.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:18:00.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:18:00.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:18:00.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:18:00.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:18:00.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:18:00.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:18:00.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:18:00.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:18:00.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:18:00.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:18:00.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:18:00.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:18:00.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:18:00.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:18:00.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:18:00.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:18:00.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:18:00.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:18:00.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:18:00.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:18:00.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:18:00.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:18:00.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:18:00.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:18:00.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:18:00.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:18:00.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:18:00.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:18:00.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:18:00.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:18:00.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:18:00.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:18:00.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:18:00.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:18:00.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:18:00.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:18:00.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:18:00.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:18:00.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:18:00.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:18:00.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:18:00.166][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:18:00.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:18:00.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:18:00.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:18:00.171][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[2023-06-05 18:18:00.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:18:00.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:18:00.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:18:00.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:18:00.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:18:00.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:18:00.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:18:00.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:18:00.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:18:00.184][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:18:00.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:18:00.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:18:00.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:18:00.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:18:00.191][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.0/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-06-05 18:18:00.204][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-06-05 18:18:00.207][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-06-05 18:18:00.208][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-06-05 18:18:00.209][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-06-05 18:18:00.211][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-06-05 18:18:00.212][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-06-05 18:18:00.214][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-06-05 18:18:00.215][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-06-05 18:18:00.217][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-06-05 18:18:00.218][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-06-05 18:18:00.219][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-06-05 18:18:00.221][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-06-05 18:18:00.222][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-06-05 18:18:00.224][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-06-05 18:18:00.225][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-06-05 18:18:00.225][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-06-05 18:18:00.225][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-06-05 18:18:00.225][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-06-05 18:18:00.225][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-06-05 18:18:00.225][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-06-05 18:18:00.225][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-06-05 18:18:00.225][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-06-05 18:18:00.225][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-06-05 18:18:00.227][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-06-05 18:18:00.228][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-06-05 18:18:00.228][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-06-05 18:18:00.230][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-06-05 18:18:00.231][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:18:00.232][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:18:00.234][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-06-05 18:18:00.235][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:18:00.236][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:18:00.238][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-06-05 18:18:00.239][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-06-05 18:18:00.239][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-06-05 18:18:00.241][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-06-05 18:18:00.242][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-06-05 18:18:00.243][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-06-05 18:18:00.245][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:18:00.253][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-06-05 18:18:00.262][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-06-05 18:18:00.291][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-06-05 18:18:00.293][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-06-05 18:18:00.298][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-06-05 18:18:00.303][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-06-05 18:18:00.308][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-06-05 18:18:00.310][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-06-05 18:18:00.312][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-06-05 18:18:00.313][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-06-05 18:18:00.334][biodb::testThat]
biodb.INFO [2023-06-05 18:18:00.335][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2023-06-05 18:18:00.337][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:18:00.338][biodb::testThat]
biodb.TRACE[2023-06-05 18:18:00.343][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/R/R-4.3.0/site-library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2023-06-05 18:18:00.349][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-06-05 18:18:00.354][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-06-05 18:18:00.364][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:18:00.365][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:18:00.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:18:00.384][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:18:00.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:18:00.386][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:18:00.388][FUN] Functions in observer BiodbConfig: [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[2023-06-05 18:18:00.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:18:00.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:18:00.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:18:00.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:18:00.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.434][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:18:00.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:18:00.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.440][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:18:00.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:18:00.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.446][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:18:00.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:18:00.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.452][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:18:00.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:18:00.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.493][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:18:00.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:18:00.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.503][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:18:00.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:18:00.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.509][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:18:00.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:18:00.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.518][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-06-05 18:18:00.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:18:00.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.524][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-06-05 18:18:00.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:18:00.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.534][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:18:00.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:18:00.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.540][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:18:00.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:18:00.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.550][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:18:00.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:00.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.556][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:18:00.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:00.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.565][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-06-05 18:18:00.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:00.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.571][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-06-05 18:18:00.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:00.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.577][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:18:00.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:00.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.583][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:18:00.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:00.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.589][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-06-05 18:18:00.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:00.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.636][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:18:00.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:00.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.642][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:18:00.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:00.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.694][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:18:00.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:00.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.700][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:18:00.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:00.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.705][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:18:00.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:00.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.715][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:18:00.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:18:00.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.720][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:18:00.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:18:00.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:18:00.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:18:00.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.732][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:18:00.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:18:00.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:18:00.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:18:00.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:18:00.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:18:00.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:18:00.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:18:00.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:18:00.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:18:00.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:18:00.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:18:00.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.770][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:18:00.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:18:00.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:18:00.775][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2023-06-05 18:18:00.782][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-06-05 18:18:00.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-06-05 18:18:00.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.788][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-06-05 18:18:00.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-06-05 18:18:00.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.794][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-06-05 18:18:00.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-06-05 18:18:00.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.800][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-06-05 18:18:00.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-06-05 18:18:00.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:18:00.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:18:00.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.847][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:18:00.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:18:00.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:18:00.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:18:00.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:18:00.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:18:00.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:18:00.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:18:00.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:18:00.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:18:00.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:18:00.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:18:00.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:18:00.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:18:00.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.896][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:18:00.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:18:00.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.902][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:18:00.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:18:00.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.907][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:18:00.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:18:00.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:18:00.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:18:00.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:18:00.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:18:00.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:18:00.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:18:00.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.948][ef$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:18:00.950][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:18:00.951][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.953][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:18:00.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:18:00.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.970][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:18:00.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:00.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.976][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:18:00.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:00.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.982][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:18:00.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:00.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.987][ef$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:18:00.989][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:00.990][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.992][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:00.993][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:18:00.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:00.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:00.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.009][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:18:01.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:18:01.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.014][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:18:01.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:18:01.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.020][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:18:01.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:18:01.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.026][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:18:01.027][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:18:01.029][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.030][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.032][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:18:01.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:18:01.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.047][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:18:01.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:18:01.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.053][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:18:01.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:18:01.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.059][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:18:01.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:18:01.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.065][ef$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:18:01.066][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:18:01.068][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.069][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.071][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:18:01.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:18:01.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.086][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:18:01.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:18:01.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.092][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:18:01.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:18:01.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.098][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:18:01.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:18:01.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.104][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:18:01.106][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:18:01.107][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.109][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.110][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:18:01.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:18:01.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.126][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:18:01.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:18:01.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.132][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:18:01.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:18:01.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.137][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:18:01.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:18:01.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.143][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:18:01.145][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:18:01.146][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.148][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.149][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:18:01.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:18:01.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.165][ef$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:18:01.166][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:18:01.168][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.169][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.177][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:18:01.179][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:18:01.180][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.182][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.190][ef$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:18:01.191][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:18:01.193][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.194][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.202][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:18:01.204][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:18:01.205][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.206][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.214][ef$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:18:01.216][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:01.217][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.219][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.227][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:18:01.228][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:18:01.230][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.231][ef$get] fields variable is a list.
biodb.INFO [2023-06-05 18:18:01.240][biodb::testThat]
biodb.INFO [2023-06-05 18:18:01.242][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-06-05 18:18:01.243][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:18:01.244][biodb::testThat]
biodb.DEBUG[2023-06-05 18:18:01.299][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2023-06-05 18:18:01.308][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2023-06-05 18:18:01.312][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2023-06-05 18:18:01.314][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-06-05 18:18:01.316][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2023-06-05 18:18:01.318][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-06-05 18:18:01.380][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-06-05 18:18:01.381][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-06-05 18:18:01.384][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:18:01.385][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:18:01.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:18:01.394][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:18:01.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:18:01.397][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:18:01.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-06-05 18:18:01.404][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:18:01.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:18:01.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:18:01.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:18:01.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.419][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:18:01.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:18:01.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.425][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:18:01.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:18:01.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.435][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:18:01.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:18:01.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.441][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:18:01.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:18:01.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.446][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:18:01.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:18:01.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.452][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:18:01.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:18:01.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.462][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:18:01.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:18:01.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.468][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:18:01.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:18:01.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.477][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-06-05 18:18:01.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:18:01.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.483][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-06-05 18:18:01.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:18:01.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.493][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:18:01.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:18:01.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.499][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:18:01.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:18:01.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.508][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:18:01.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:01.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.514][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:18:01.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:01.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.523][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-06-05 18:18:01.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:01.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.529][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-06-05 18:18:01.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:01.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.535][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:18:01.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:01.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.541][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:18:01.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:01.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.546][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-06-05 18:18:01.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:01.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.556][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:18:01.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:01.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.562][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:18:01.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:01.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.568][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:18:01.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:01.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.573][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:18:01.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:01.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.579][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:18:01.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:01.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.597][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:18:01.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:18:01.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.603][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:18:01.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:18:01.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:18:01.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:18:01.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.614][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:18:01.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:18:01.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:18:01.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:18:01.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:18:01.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:18:01.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:18:01.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:18:01.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:18:01.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:18:01.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.647][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:18:01.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:18:01.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:18:01.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:18:01.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:18:01.658][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2023-06-05 18:18:01.660][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-06-05 18:18:01.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-06-05 18:18:01.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.665][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-06-05 18:18:01.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-06-05 18:18:01.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.671][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-06-05 18:18:01.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-06-05 18:18:01.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-06-05 18:18:01.684][biodb::testThat]
biodb.INFO [2023-06-05 18:18:01.686][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2023-06-05 18:18:01.687][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:18:01.688][biodb::testThat]
biodb.TRACE[2023-06-05 18:18:01.692][ef$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:18:01.694][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:01.695][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.697][ef$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:18:01.698][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2023-06-05 18:18:01.738][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:18:01.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:01.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.743][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:18:01.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:01.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:01.749][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:18:01.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:01.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:01.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:18:01.757][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-06-05 18:18:01.774][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[2023-06-05 18:18:01.803][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-06-05 18:18:01.804][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-06-05 18:18:01.807][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2023-06-05 18:18:02.912][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2023-06-05 18:18:03.877][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-06-05 18:18:03.894][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2023-06-05 18:18:03.946][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2023-06-05 18:18:03.957][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2023-06-05 18:18:03.992][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:18:03.995][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:18:03.997][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:03.999][ef$get] fields variable is a list.
biodb.INFO [2023-06-05 18:18:04.004][biodb::testThat]
biodb.INFO [2023-06-05 18:18:04.006][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2023-06-05 18:18:04.007][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:18:04.009][biodb::testThat]
biodb.TRACE[2023-06-05 18:18:04.157][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:18:04.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:04.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:04.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:04.166][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:18:04.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:04.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:04.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:04.174][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:18:04.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:04.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:04.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:18:04.363][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-06-05 18:18:04.367][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-06-05 18:18:04.391][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-06-05 18:18:04.393][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-06-05 18:18:04.395][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2023-06-05 18:18:04.426][biodb::testThat]
biodb.INFO [2023-06-05 18:18:04.427][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2023-06-05 18:18:04.428][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:18:04.430][biodb::testThat]
biodb.TRACE[2023-06-05 18:18:04.468][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-06-05 18:18:04.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-06-05 18:18:04.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:04.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:04.473][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-06-05 18:18:04.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-06-05 18:18:04.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:04.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:04.479][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-06-05 18:18:04.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-06-05 18:18:04.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:04.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:04.484][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-06-05 18:18:04.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-06-05 18:18:04.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:04.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:04.551][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-06-05 18:18:04.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-06-05 18:18:04.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:04.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:04.557][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-06-05 18:18:04.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-06-05 18:18:04.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:04.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:04.563][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-06-05 18:18:04.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-06-05 18:18:04.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:04.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:04.568][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-06-05 18:18:04.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-06-05 18:18:04.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:04.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-06-05 18:18:04.577][biodb::testThat]
biodb.INFO [2023-06-05 18:18:04.579][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-06-05 18:18:04.580][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:18:04.581][biodb::testThat]
biodb.INFO [2023-06-05 18:18:04.588][biodb::testThat]
biodb.INFO [2023-06-05 18:18:04.589][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-06-05 18:18:04.591][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:18:04.592][biodb::testThat]
biodb.INFO [2023-06-05 18:18:04.598][biodb::testThat]
biodb.INFO [2023-06-05 18:18:04.600][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2023-06-05 18:18:04.601][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:18:04.602][biodb::testThat]
biodb.DEBUG[2023-06-05 18:18:04.607][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2023-06-05 18:18:05.872][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2023-06-05 18:18:06.562][biodb::testThat]
biodb.INFO [2023-06-05 18:18:06.563][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2023-06-05 18:18:06.565][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:18:06.566][biodb::testThat]
biodb.TRACE[2023-06-05 18:18:06.589][ef$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:18:06.591][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:06.592][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:06.593][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:06.595][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:18:06.596][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:18:06.597][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:06.599][ef$get] fields variable is a list.
biodb.INFO [2023-06-05 18:18:06.601][biodb::testThat]
biodb.INFO [2023-06-05 18:18:06.602][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2023-06-05 18:18:06.604][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:18:06.605][biodb::testThat]
biodb.TRACE[2023-06-05 18:18:06.629][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:18:06.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:06.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:06.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:06.635][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:18:06.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:06.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:06.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:06.641][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:18:06.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:18:06.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:06.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:18:06.768][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-06-05 18:18:06.772][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-06-05 18:18:06.774][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-06-05 18:18:06.776][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-06-05 18:18:06.778][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2023-06-05 18:18:06.898][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-06-05 18:18:06.903][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-06-05 18:18:06.905][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-06-05 18:18:06.906][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-06-05 18:18:06.908][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2023-06-05 18:18:06.931][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-06-05 18:18:06.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-06-05 18:18:06.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:06.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:06.952][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-06-05 18:18:06.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-06-05 18:18:06.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:06.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:06.973][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:18:06.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:18:06.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:06.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:06.979][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:18:06.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:18:06.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:06.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:06.985][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:18:06.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:18:06.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:06.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:06.991][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:18:06.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:18:06.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:06.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:18:06.997][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:18:06.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:18:07.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:18:07.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:18:07.052][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2023-06-05 18:18:07.075][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-06-05 18:18:07.077][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-06-05 18:18:07.109][private$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[2023-06-05 18:18:12.109][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[2023-06-05 18:19:05.608][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-06-05 18:19:05.618][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2023-06-05 18:19:05.656][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2023-06-05 18:19:06.871][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[2023-06-05 18:19:06.876][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-06-05 18:19:06.878][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-06-05 18:19:06.880][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2023-06-05 18:19:07.821][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2023-06-05 18:19:08.759][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-06-05 18:19:08.769][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2023-06-05 18:19:08.785][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2023-06-05 18:19:08.886][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2023-06-05 18:19:08.891][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-06-05 18:19:08.892][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-06-05 18:19:08.895][private$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[2023-06-05 18:19:09.832][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[2023-06-05 18:19:10.784][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-06-05 18:19:10.794][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2023-06-05 18:19:10.809][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2023-06-05 18:19:10.841][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-06-05 18:19:10.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-06-05 18:19:10.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:10.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-06-05 18:19:10.862][biodb::testThat]
biodb.INFO [2023-06-05 18:19:10.863][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2023-06-05 18:19:10.865][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:19:10.866][biodb::testThat]
biodb.TRACE[2023-06-05 18:19:10.870][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-06-05 18:19:10.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-06-05 18:19:10.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:10.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:10.876][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-06-05 18:19:10.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-06-05 18:19:10.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:10.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:10.903][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:19:10.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:19:10.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:10.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:10.908][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:19:10.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:19:10.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:10.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:10.914][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:19:10.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:19:10.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:10.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:10.919][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:19:10.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:19:10.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:10.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:19:10.935][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:19:10.937][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:19:10.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:19:10.946][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:19:10.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:19:10.948][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:19:10.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:19:11.004][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[2023-06-05 18:19:11.009][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-06-05 18:19:11.011][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-06-05 18:19:11.013][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2023-06-05 18:19:15.250][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2023-06-05 18:19:29.842][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-06-05 18:19:29.853][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2023-06-05 18:19:29.891][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2023-06-05 18:19:30.956][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2023-06-05 18:19:31.025][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-06-05 18:19:31.027][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2023-06-05 18:19:31.029][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2023-06-05 18:19:31.031][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-06-05 18:19:31.032][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-06-05 18:19:31.034][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-06-05 18:19:31.035][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-06-05 18:19:31.036][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-06-05 18:19:31.059][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:19:31.060][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:19:31.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:19:31.070][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:19:31.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:19:31.073][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:19:31.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:19:31.076][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2023-06-05 18:19:31.080][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-06-05 18:19:31.081][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-06-05 18:19:31.083][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2023-06-05 18:19:32.023][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2023-06-05 18:19:33.006][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-06-05 18:19:33.016][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2023-06-05 18:19:33.032][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2023-06-05 18:19:33.039][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:19:33.040][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:19:33.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:19:33.050][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:19:33.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:19:33.053][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:19:33.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:19:33.056][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2023-06-05 18:19:33.060][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-06-05 18:19:33.061][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-06-05 18:19:33.063][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2023-06-05 18:19:33.922][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2023-06-05 18:19:34.846][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-06-05 18:19:34.856][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2023-06-05 18:19:34.870][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2023-06-05 18:19:34.884][private$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[2023-06-05 18:19:34.889][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-06-05 18:19:34.914][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-06-05 18:19:34.916][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-06-05 18:19:34.918][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:19:34.920][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:19:34.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:19:34.929][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:19:34.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:19:34.932][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:19:34.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-06-05 18:19:34.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:19:34.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:19:34.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:34.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:34.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:19:34.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:19:34.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:34.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:34.976][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:19:34.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:19:34.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:34.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.019][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:19:35.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:19:35.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.029][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:19:35.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:19:35.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.034][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:19:35.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:19:35.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.040][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:19:35.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:19:35.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.046][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:19:35.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:19:35.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.055][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:19:35.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:19:35.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.061][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:19:35.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:19:35.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.070][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-06-05 18:19:35.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:19:35.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.076][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-06-05 18:19:35.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:19:35.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.085][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:19:35.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:19:35.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.091][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:19:35.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:19:35.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.100][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:19:35.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:19:35.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.106][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:19:35.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:19:35.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.116][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-06-05 18:19:35.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:19:35.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.122][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-06-05 18:19:35.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:19:35.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.127][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:19:35.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:19:35.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.133][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:19:35.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:19:35.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.139][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-06-05 18:19:35.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:19:35.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.148][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.154][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:19:35.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:19:35.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.183][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:19:35.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:19:35.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:19:35.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:19:35.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:19:35.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:19:35.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:19:35.209][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:19:35.211][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:19:35.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:19:35.221][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:19:35.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:19:35.224][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:19:35.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-06-05 18:19:35.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:19:35.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:19:35.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:19:35.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:19:35.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.247][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:19:35.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:19:35.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.252][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:19:35.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:19:35.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.258][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:19:35.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:19:35.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.264][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:19:35.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:19:35.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.270][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:19:35.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:19:35.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.279][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:19:35.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:19:35.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.285][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:19:35.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:19:35.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.295][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-06-05 18:19:35.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:19:35.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.300][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-06-05 18:19:35.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:19:35.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.310][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:19:35.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:19:35.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.316][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:19:35.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:19:35.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.325][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:19:35.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:19:35.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.331][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:19:35.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:19:35.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.340][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-06-05 18:19:35.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:19:35.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.346][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-06-05 18:19:35.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:19:35.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.352][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:19:35.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:19:35.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.358][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:19:35.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:19:35.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.364][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-06-05 18:19:35.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:19:35.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.373][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.397][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:19:35.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:19:35.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.408][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:19:35.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:19:35.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:19:35.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:19:35.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:19:35.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:19:35.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:19:35.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:19:35.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:19:35.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:19:35.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.447][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:19:35.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:19:35.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:19:35.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:19:35.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.459][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:19:35.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:19:35.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.464][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:19:35.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:19:35.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:19:35.470][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2023-06-05 18:19:35.483][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-06-05 18:19:35.486][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:19:35.487][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:19:35.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:19:35.496][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:19:35.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:19:35.499][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:19:35.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-06-05 18:19:35.502][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.507][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.513][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:19:35.514][private$selectFields]
biodb.TRACE[2023-06-05 18:19:35.516][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-06-05 18:19:35.517][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-06-05 18:19:35.518][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:19:35.520][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.521][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.522][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.524][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.525][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.527][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.528][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.529][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.531][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:19:35.532][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:19:35.534][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.535][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.536][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.538][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.539][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-06-05 18:19:35.540][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.546][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.552][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.571][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-06-05 18:19:35.572][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:19:35.574][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:19:35.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:19:35.583][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:19:35.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:19:35.586][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:19:35.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-06-05 18:19:35.589][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.612][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.618][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:19:35.619][private$selectFields]
biodb.TRACE[2023-06-05 18:19:35.620][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-06-05 18:19:35.622][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-06-05 18:19:35.624][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:19:35.626][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.627][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.629][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.630][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.632][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.633][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.634][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.636][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.637][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:19:35.638][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:19:35.640][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.641][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.643][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.644][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.645][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-06-05 18:19:35.647][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.652][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.658][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.664][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-06-05 18:19:35.665][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:19:35.667][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:19:35.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:19:35.676][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:19:35.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:19:35.679][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:19:35.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-06-05 18:19:35.682][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.687][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.693][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:19:35.694][private$selectFields]
biodb.TRACE[2023-06-05 18:19:35.696][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-06-05 18:19:35.697][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-06-05 18:19:35.698][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:19:35.700][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.701][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.703][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.704][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.705][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.707][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.708][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.710][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.711][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:19:35.712][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:19:35.714][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.715][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.717][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.718][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.720][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-06-05 18:19:35.721][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.727][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.732][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:19:35.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.738][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-06-05 18:19:35.740][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-06-05 18:19:35.741][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-06-05 18:19:35.754][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-06-05 18:19:35.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-06-05 18:19:35.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-06-05 18:19:35.762][biodb::testThat]
biodb.INFO [2023-06-05 18:19:35.763][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2023-06-05 18:19:35.764][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:19:35.766][biodb::testThat]
biodb.TRACE[2023-06-05 18:19:35.770][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-06-05 18:19:35.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-06-05 18:19:35.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.776][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-06-05 18:19:35.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-06-05 18:19:35.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.781][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:19:35.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:19:35.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.787][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:19:35.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:19:35.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.793][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:19:35.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:19:35.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:19:35.799][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:19:35.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:19:35.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:19:35.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:19:35.932][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:19:35.934][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:19:35.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:19:35.945][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:19:35.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:19:35.948][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:19:35.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:19:36.009][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[2023-06-05 18:19:36.015][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-06-05 18:19:36.016][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-06-05 18:19:36.019][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.TRACE[2023-06-05 18:19:40.872][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375).
biodb.DEBUG[2023-06-05 18:20:01.843][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-06-05 18:20:01.856][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2023-06-05 18:20:01.894][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2023-06-05 18:20:03.151][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-06-05 18:20:03.184][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:20:03.186][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:20:03.187][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:20:03.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:20:03.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:20:03.197][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:20:03.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-06-05 18:20:03.217][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:03.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:03.222][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:03.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:03.257][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:20:03.258][private$selectFields]
biodb.TRACE[2023-06-05 18:20:03.260][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-06-05 18:20:03.261][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-06-05 18:20:03.262][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:20:03.264][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.265][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.266][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:03.268][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:03.269][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.270][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.272][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:03.273][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:03.274][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:20:03.319][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:20:03.320][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.322][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.323][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:03.324][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:03.325][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-06-05 18:20:03.327][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:03.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:03.332][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:03.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:03.338][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:03.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:03.343][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-06-05 18:20:03.345][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:20:03.346][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:20:03.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:20:03.355][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:20:03.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:20:03.357][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:20:03.359][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".
biodb.TRACE[2023-06-05 18:20:03.360][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:03.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:03.366][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:03.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:03.371][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:20:03.373][private$selectFields]
biodb.TRACE[2023-06-05 18:20:03.374][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-06-05 18:20:03.375][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-06-05 18:20:03.377][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:20:03.378][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.379][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.381][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:03.382][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:03.384][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.385][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.387][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:03.388][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:03.390][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:20:03.391][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:20:03.393][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.394][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.396][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:03.397][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:03.398][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-06-05 18:20:03.400][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:03.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:03.406][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:03.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:03.412][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:03.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:03.418][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-06-05 18:20:03.419][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:20:03.420][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:20:03.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:20:03.429][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:20:03.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:20:03.432][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:20:03.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-06-05 18:20:03.435][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:03.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:03.441][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:03.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:03.447][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:20:03.448][private$selectFields]
biodb.TRACE[2023-06-05 18:20:03.449][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-06-05 18:20:03.451][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-06-05 18:20:03.452][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:20:03.453][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.455][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.456][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:03.457][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:03.459][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.460][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.462][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:03.463][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:03.464][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:20:03.466][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:20:03.467][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.468][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.470][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:03.471][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:03.472][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-06-05 18:20:03.474][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:03.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:03.480][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:03.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:03.485][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:03.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:03.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:03.491][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-06-05 18:20:03.492][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-06-05 18:20:03.494][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-06-05 18:20:03.505][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-06-05 18:20:03.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-06-05 18:20:03.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:03.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-06-05 18:20:03.512][biodb::testThat]
biodb.INFO [2023-06-05 18:20:03.513][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2023-06-05 18:20:03.515][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:20:03.516][biodb::testThat]
biodb.TRACE[2023-06-05 18:20:03.533][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-06-05 18:20:03.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-06-05 18:20:03.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:03.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:03.539][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-06-05 18:20:03.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-06-05 18:20:03.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:03.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:03.544][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:20:03.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:20:03.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:03.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:03.549][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:20:03.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:20:03.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:03.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:03.555][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:20:03.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:20:03.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:03.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:03.560][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:20:03.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:20:03.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:03.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:20:03.577][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:20:03.578][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:20:03.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:20:03.587][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:20:03.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:20:03.590][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:20:03.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:20:03.644][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2023-06-05 18:20:03.648][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-06-05 18:20:03.650][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2023-06-05 18:20:03.652][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-06-05 18:20:03.738][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2023-06-05 18:20:04.762][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-06-05 18:20:04.765][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:20:04.767][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:20:04.768][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:20:04.777][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:20:04.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:20:04.780][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:20:04.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-06-05 18:20:04.784][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:04.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:04.789][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:04.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:04.795][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:20:04.797][private$selectFields]
biodb.TRACE[2023-06-05 18:20:04.798][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-06-05 18:20:04.799][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-06-05 18:20:04.801][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:20:04.802][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.804][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.805][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:04.807][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:04.808][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.810][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.811][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:04.813][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:04.814][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:20:04.816][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:20:04.817][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.819][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.820][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:04.822][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:04.823][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-06-05 18:20:04.825][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:04.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:04.831][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:04.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:04.837][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:04.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:04.871][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-06-05 18:20:04.873][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:20:04.874][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:20:04.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:20:04.884][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:20:04.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:20:04.886][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:20:04.888][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.TRACE[2023-06-05 18:20:04.889][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:04.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:04.895][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:04.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:04.901][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:20:04.902][private$selectFields]
biodb.TRACE[2023-06-05 18:20:04.904][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-06-05 18:20:04.905][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-06-05 18:20:04.907][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:20:04.908][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.910][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.911][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:04.912][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:04.914][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.915][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.917][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:04.918][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:04.919][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:20:04.921][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:20:04.922][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.924][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.925][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:04.926][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:04.928][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-06-05 18:20:04.929][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:04.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:04.935][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:04.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:04.941][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:04.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:04.948][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-06-05 18:20:04.950][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:20:04.951][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:20:04.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:20:04.961][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:20:04.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:20:04.963][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:20:04.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-06-05 18:20:04.966][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:04.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:04.972][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:04.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:04.978][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:20:04.979][private$selectFields]
biodb.TRACE[2023-06-05 18:20:04.981][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-06-05 18:20:04.982][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-06-05 18:20:04.983][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:20:04.985][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.986][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.988][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:04.989][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:04.991][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.992][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:04.994][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:04.995][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:04.996][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:20:04.998][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:20:04.999][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:05.001][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:05.002][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:05.003][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:05.005][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-06-05 18:20:05.006][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:05.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:05.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:05.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:05.012][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:05.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:05.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:05.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:05.017][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:05.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:05.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:05.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:05.023][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-06-05 18:20:05.024][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-06-05 18:20:05.025][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-06-05 18:20:05.055][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-06-05 18:20:05.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-06-05 18:20:05.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:05.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-06-05 18:20:05.062][biodb::testThat]
biodb.INFO [2023-06-05 18:20:05.064][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2023-06-05 18:20:05.065][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:20:05.066][biodb::testThat]
biodb.DEBUG[2023-06-05 18:20:05.069][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2023-06-05 18:20:05.070][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2023-06-05 18:20:05.073][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2023-06-05 18:20:05.075][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-06-05 18:20:05.091][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-06-05 18:20:05.093][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-06-05 18:20:05.094][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-06-05 18:20:05.096][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-06-05 18:20:05.097][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-06-05 18:20:05.117][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:20:05.118][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:20:05.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:20:05.127][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:20:05.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:20:05.130][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:20:05.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:20:05.133][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2023-06-05 18:20:05.136][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-06-05 18:20:05.138][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-06-05 18:20:05.139][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-06-05 18:20:06.058][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-06-05 18:20:06.060][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-06-05 18:20:06.061][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-06-05 18:20:06.062][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-06-05 18:20:07.094][private$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[2023-06-05 18:20:07.095][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-06-05 18:20:07.096][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-06-05 18:20:07.098][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-06-05 18:20:07.997][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-06-05 18:20:07.998][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-06-05 18:20:07.999][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-06-05 18:20:08.001][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-06-05 18:20:09.031][private$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[2023-06-05 18:20:09.033][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-06-05 18:20:09.034][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-06-05 18:20:09.036][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-06-05 18:20:09.934][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-06-05 18:20:09.935][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-06-05 18:20:09.937][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-06-05 18:20:09.938][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-06-05 18:20:10.969][private$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[2023-06-05 18:20:10.970][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-06-05 18:20:10.972][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-06-05 18:20:10.973][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-06-05 18:20:11.869][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-06-05 18:20:11.870][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-06-05 18:20:11.872][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-06-05 18:20:11.873][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-06-05 18:20:12.906][private$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[2023-06-05 18:20:12.907][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-06-05 18:20:12.909][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-06-05 18:20:12.910][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-06-05 18:20:13.820][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-06-05 18:20:13.821][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-06-05 18:20:13.823][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-06-05 18:20:13.824][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-06-05 18:20:14.856][private$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[2023-06-05 18:20:14.858][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-06-05 18:20:14.860][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-06-05 18:20:14.861][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-06-05 18:20:15.751][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-06-05 18:20:15.753][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-06-05 18:20:15.754][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-06-05 18:20:15.755][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-06-05 18:20:16.786][private$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[2023-06-05 18:20:16.788][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-06-05 18:20:16.789][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-06-05 18:20:16.791][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-06-05 18:20:17.701][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-06-05 18:20:17.702][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-06-05 18:20:17.704][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-06-05 18:20:17.705][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-06-05 18:20:18.737][private$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[2023-06-05 18:20:18.739][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-06-05 18:20:18.740][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-06-05 18:20:18.742][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-06-05 18:20:19.615][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-06-05 18:20:19.617][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-06-05 18:20:19.618][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-06-05 18:20:19.619][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-06-05 18:20:20.674][private$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[2023-06-05 18:20:20.676][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-06-05 18:20:20.677][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-06-05 18:20:20.679][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-06-05 18:20:21.585][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-06-05 18:20:21.586][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-06-05 18:20:21.588][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-06-05 18:20:21.590][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-06-05 18:20:22.621][private$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[2023-06-05 18:20:22.622][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-06-05 18:20:22.624][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-06-05 18:20:22.625][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-06-05 18:20:23.540][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-06-05 18:20:23.542][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-06-05 18:20:23.543][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-06-05 18:20:23.545][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-06-05 18:20:24.576][private$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[2023-06-05 18:20:24.586][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2023-06-05 18:20:24.591][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-06-05 18:20:24.614][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-06-05 18:20:24.615][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-06-05 18:20:24.618][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:20:24.619][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:20:24.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:20:24.628][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:20:24.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:20:24.631][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:20:24.632][FUN] Functions in observer BiodbConfig: [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[2023-06-05 18:20:24.635][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:24.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:24.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:24.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:24.640][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:24.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:24.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:24.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:24.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:20:24.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:20:24.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:24.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:24.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:20:24.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:20:24.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:24.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:24.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:20:24.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:20:24.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:24.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:24.663][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:20:24.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:20:24.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:24.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:24.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:20:24.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:20:24.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:24.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:24.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:20:24.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:20:24.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:24.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:20:24.700][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2023-06-05 18:20:24.701][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2023-06-05 18:20:24.710][biodb::testThat]
biodb.INFO [2023-06-05 18:20:24.712][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2023-06-05 18:20:24.713][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:20:24.714][biodb::testThat]
biodb.DEBUG[2023-06-05 18:20:24.725][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2023-06-05 18:20:24.727][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2023-06-05 18:20:24.728][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-06-05 18:20:24.730][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2023-06-05 18:20:24.732][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2023-06-05 18:20:24.733][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-06-05 18:20:24.735][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-06-05 18:20:24.736][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-06-05 18:20:24.738][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-06-05 18:20:24.739][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-06-05 18:20:24.744][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:20:24.746][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:20:24.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:20:24.755][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:20:24.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:20:24.758][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:20:24.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:20:24.760][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2023-06-05 18:20:24.764][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-06-05 18:20:24.766][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-06-05 18:20:24.767][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-06-05 18:20:25.645][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-06-05 18:20:25.647][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-06-05 18:20:25.648][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[2023-06-05 18:20:25.649][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-06-05 18:20:26.681][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-06-05 18:20:26.682][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-06-05 18:20:26.684][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-06-05 18:20:26.685][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-06-05 18:20:28.981][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-06-05 18:20:28.982][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-06-05 18:20:28.984][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[2023-06-05 18:20:28.985][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-06-05 18:20:30.017][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-06-05 18:20:30.018][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-06-05 18:20:30.019][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-06-05 18:20:30.021][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-06-05 18:20:30.927][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-06-05 18:20:30.929][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-06-05 18:20:30.930][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[2023-06-05 18:20:30.932][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-06-05 18:20:31.986][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-06-05 18:20:31.988][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-06-05 18:20:31.989][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-06-05 18:20:31.991][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-06-05 18:20:32.904][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-06-05 18:20:32.905][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-06-05 18:20:32.907][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[2023-06-05 18:20:32.908][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-06-05 18:20:33.940][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-06-05 18:20:33.941][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-06-05 18:20:33.943][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-06-05 18:20:33.945][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-06-05 18:20:34.879][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-06-05 18:20:34.880][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-06-05 18:20:34.881][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[2023-06-05 18:20:34.883][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-06-05 18:20:35.915][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-06-05 18:20:35.917][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-06-05 18:20:35.918][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-06-05 18:20:35.920][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-06-05 18:20:40.429][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-06-05 18:20:40.430][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-06-05 18:20:40.432][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[2023-06-05 18:20:40.433][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-06-05 18:20:41.465][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-06-05 18:20:41.467][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-06-05 18:20:41.468][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-06-05 18:20:41.470][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-06-05 18:20:42.375][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-06-05 18:20:42.376][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-06-05 18:20:42.377][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[2023-06-05 18:20:42.379][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-06-05 18:20:43.410][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-06-05 18:20:43.412][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-06-05 18:20:43.414][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-06-05 18:20:43.416][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-06-05 18:20:44.322][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-06-05 18:20:44.323][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-06-05 18:20:44.325][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[2023-06-05 18:20:44.326][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-06-05 18:20:45.358][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-06-05 18:20:45.360][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-06-05 18:20:45.361][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-06-05 18:20:45.363][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-06-05 18:20:46.247][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-06-05 18:20:46.248][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-06-05 18:20:46.250][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[2023-06-05 18:20:46.252][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-06-05 18:20:47.283][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-06-05 18:20:47.285][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-06-05 18:20:47.287][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-06-05 18:20:47.289][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-06-05 18:20:48.171][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-06-05 18:20:48.173][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-06-05 18:20:48.174][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[2023-06-05 18:20:48.175][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-06-05 18:20:49.206][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-06-05 18:20:49.207][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:20:49.209][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:20:49.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:20:49.218][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:20:49.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:20:49.220][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:20:49.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:20:49.223][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2023-06-05 18:20:49.226][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-06-05 18:20:49.228][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-06-05 18:20:49.230][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2023-06-05 18:20:50.154][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.DEBUG[2023-06-05 18:20:51.149][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-06-05 18:20:51.158][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.content"
biodb.TRACE[2023-06-05 18:20:51.173][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.request"
biodb.TRACE[2023-06-05 18:20:51.186][private$doSaveContentToFile] Saving to cache [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv"
biodb.DEBUG[2023-06-05 18:20:51.192][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-06-05 18:20:51.215][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-06-05 18:20:51.217][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-06-05 18:20:51.219][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:20:51.220][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:20:51.222][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:20:51.229][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:20:51.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:20:51.232][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:20:51.233][FUN] Functions in observer BiodbConfig: [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[2023-06-05 18:20:51.236][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:51.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:51.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.241][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:51.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:51.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:20:51.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:20:51.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:20:51.252][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:20:51.253][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:20:51.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:20:51.262][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:20:51.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:20:51.265][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:20:51.266][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.TRACE[2023-06-05 18:20:51.272][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:20:51.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:20:51.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:20:51.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:20:51.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.287][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:20:51.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:20:51.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.292][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:20:51.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:20:51.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.302][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:20:51.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:20:51.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.307][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:20:51.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:20:51.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.317][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:20:51.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:20:51.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.322][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:20:51.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:20:51.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.332][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:20:51.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:20:51.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.354][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:20:51.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:20:51.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.363][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:20:51.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:20:51.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.368][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:20:51.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:20:51.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.377][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-06-05 18:20:51.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:20:51.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.383][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-06-05 18:20:51.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:20:51.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.392][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:20:51.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:20:51.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.398][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:20:51.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:20:51.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.407][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:20:51.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:20:51.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.412][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:20:51.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:20:51.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.421][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-06-05 18:20:51.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:20:51.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.427][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-06-05 18:20:51.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:20:51.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.432][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:20:51.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:20:51.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.438][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:20:51.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:20:51.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.443][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-06-05 18:20:51.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:20:51.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.453][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:20:51.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:20:51.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.458][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:20:51.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:20:51.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.464][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:20:51.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:20:51.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.469][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:20:51.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:20:51.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.475][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:20:51.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:20:51.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.484][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:51.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:51.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.489][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:51.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:51.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:20:51.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:20:51.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.500][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:51.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:20:51.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:20:51.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:20:51.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:20:51.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:20:51.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:20:51.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:20:51.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:20:51.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:20:51.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:20:51.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:20:51.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:20:51.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:20:51.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:20:51.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:20:51.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.565][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:20:51.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:20:51.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:20:51.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:20:51.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:20:51.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:20:51.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:20:51.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:20:51.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:20:51.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:20:51.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:20:51.587][self$createEntryFromContent] Accession numbers: NA, LMFA08040013.
biodb.DEBUG[2023-06-05 18:20:51.588][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2023-06-05 18:20:51.590][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2023-06-05 18:20:51.606][biodb::testThat]
biodb.INFO [2023-06-05 18:20:51.607][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2023-06-05 18:20:51.608][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:20:51.610][biodb::testThat]
biodb.INFO [2023-06-05 18:20:51.637][biodb::testThat]
biodb.INFO [2023-06-05 18:20:51.638][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2023-06-05 18:20:51.640][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:20:51.641][biodb::testThat]
biodb.INFO [2023-06-05 18:20:51.650][biodb::testThat]
biodb.INFO [2023-06-05 18:20:51.652][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2023-06-05 18:20:51.653][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:20:51.654][biodb::testThat]
biodb.DEBUG[2023-06-05 18:20:51.659][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[2023-06-05 18:20:51.663][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-06-05 18:20:51.665][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-06-05 18:20:51.667][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2023-06-05 18:20:55.796][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2023-06-05 18:21:27.174][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-06-05 18:21:27.188][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2023-06-05 18:21:27.227][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2023-06-05 18:21:28.245][ef$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:21:28.246][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:21:28.248][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:21:28.249][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:21:28.250][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:21:28.252][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:21:28.253][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:21:28.254][ef$get] fields variable is a list.
biodb.INFO [2023-06-05 18:21:28.257][biodb::testThat]
biodb.INFO [2023-06-05 18:21:28.258][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2023-06-05 18:21:28.259][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:21:28.261][biodb::testThat]
biodb.ERROR[2023-06-05 18:21:28.287][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2023-06-05 18:21:28.312][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2023-06-05 18:21:28.328][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-06-05 18:21:28.330][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-06-05 18:21:28.332][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-06-05 18:21:28.333][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-06-05 18:21:28.334][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:21:28.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:21:28.337][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:21:28.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:21:28.340][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:28.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-06-05 18:21:28.358][biodb::testContext]
biodb.INFO [2023-06-05 18:21:28.359][biodb::testContext] ********************************************************************************
biodb.INFO [2023-06-05 18:21:28.361][biodb::testContext] Test context - Web services tests
biodb.INFO [2023-06-05 18:21:28.362][biodb::testContext] ********************************************************************************
biodb.INFO [2023-06-05 18:21:28.364][biodb::testContext]
biodb.INFO [2023-06-05 18:21:28.371][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.9.0.
biodb.DEBUG[2023-06-05 18:21:28.374][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.0/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-06-05 18:21:28.379][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-06-05 18:21:28.381][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-06-05 18:21:28.383][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-06-05 18:21:28.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:28.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:28.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:28.388][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-06-05 18:21:28.390][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-06-05 18:21:28.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:28.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:28.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:28.395][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-06-05 18:21:28.397][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-06-05 18:21:28.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:28.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:28.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:28.402][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-06-05 18:21:28.404][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-06-05 18:21:28.405][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-06-05 18:21:28.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:28.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:28.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:28.411][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-06-05 18:21:28.412][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-06-05 18:21:28.414][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-06-05 18:21:28.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:28.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:28.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:28.419][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-06-05 18:21:28.421][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-06-05 18:21:28.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:28.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:28.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:28.426][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-06-05 18:21:28.428][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-06-05 18:21:28.430][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-06-05 18:21:28.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:28.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:28.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:28.435][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-06-05 18:21:28.437][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-06-05 18:21:28.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:28.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:28.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:28.442][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-06-05 18:21:28.444][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-06-05 18:21:28.446][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-06-05 18:21:28.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:28.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:28.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:28.477][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-06-05 18:21:28.478][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-06-05 18:21:28.480][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-06-05 18:21:28.481][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-06-05 18:21:28.483][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-06-05 18:21:28.484][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-06-05 18:21:28.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:28.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:28.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:28.490][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-06-05 18:21:28.491][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-06-05 18:21:28.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:28.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:28.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:28.496][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-06-05 18:21:28.498][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-06-05 18:21:28.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:28.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:28.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:28.503][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-06-05 18:21:28.505][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-06-05 18:21:28.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:28.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:28.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:28.510][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-06-05 18:21:28.512][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-06-05 18:21:28.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:28.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:28.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:28.517][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-06-05 18:21:28.518][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-06-05 18:21:28.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:28.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:28.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:28.523][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-06-05 18:21:28.525][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-06-05 18:21:28.529][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-06-05 18:21:28.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:28.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:28.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:28.534][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-06-05 18:21:28.536][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-06-05 18:21:28.537][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-06-05 18:21:28.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:28.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:28.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:28.542][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-06-05 18:21:28.545][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-06-05 18:21:28.546][self$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[2023-06-05 18:21:28.547][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-06-05 18:21:28.549][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-06-05 18:21:28.550][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-06-05 18:21:28.552][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-06-05 18:21:28.553][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-06-05 18:21:28.554][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-06-05 18:21:28.556][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-06-05 18:21:28.557][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-06-05 18:21:28.558][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-06-05 18:21:28.560][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-06-05 18:21:28.561][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-06-05 18:21:28.563][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:21:28.564][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-06-05 18:21:28.566][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-06-05 18:21:28.566][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-06-05 18:21:28.566][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-06-05 18:21:28.566][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-06-05 18:21:28.566][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-06-05 18:21:28.567][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-06-05 18:21:28.568][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:21:28.570][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:21:28.571][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-06-05 18:21:28.572][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:21:28.573][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:21:28.575][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-06-05 18:21:28.576][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:21:28.577][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-06-05 18:21:28.579][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-06-05 18:21:28.580][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-06-05 18:21:28.581][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:21:28.583][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-06-05 18:21:28.585][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-06-05 18:21:28.587][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-06-05 18:21:28.588][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-06-05 18:21:28.589][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-06-05 18:21:28.591][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-06-05 18:21:28.592][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-06-05 18:21:28.594][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-06-05 18:21:28.595][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-06-05 18:21:28.596][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-06-05 18:21:28.598][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-06-05 18:21:28.599][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-06-05 18:21:28.600][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-06-05 18:21:28.602][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-06-05 18:21:28.603][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:21:28.604][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-06-05 18:21:28.606][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-06-05 18:21:28.606][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-06-05 18:21:28.606][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-06-05 18:21:28.606][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-06-05 18:21:28.606][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-06-05 18:21:28.607][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-06-05 18:21:28.609][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:21:28.610][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:21:28.611][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-06-05 18:21:28.612][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:21:28.614][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:21:28.615][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-06-05 18:21:28.616][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:21:28.618][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-06-05 18:21:28.619][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-06-05 18:21:28.620][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-06-05 18:21:28.621][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:21:28.623][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-06-05 18:21:28.626][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-06-05 18:21:28.627][self$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[2023-06-05 18:21:28.628][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-06-05 18:21:28.630][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-06-05 18:21:28.631][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-06-05 18:21:28.632][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-06-05 18:21:28.634][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-06-05 18:21:28.635][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-06-05 18:21:28.637][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-06-05 18:21:28.638][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-06-05 18:21:28.639][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-06-05 18:21:28.641][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-06-05 18:21:28.642][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-06-05 18:21:28.644][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:21:28.645][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-06-05 18:21:28.646][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:21:28.648][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-06-05 18:21:28.649][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:21:28.650][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:21:28.652][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-06-05 18:21:28.653][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:21:28.654][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:21:28.656][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-06-05 18:21:28.657][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:21:28.658][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-06-05 18:21:28.660][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-06-05 18:21:28.661][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-06-05 18:21:28.662][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:21:28.680][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-06-05 18:21:28.682][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-06-05 18:21:28.684][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-06-05 18:21:28.685][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-06-05 18:21:28.686][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-06-05 18:21:28.688][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-06-05 18:21:28.689][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-06-05 18:21:28.690][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-06-05 18:21:28.692][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-06-05 18:21:28.693][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-06-05 18:21:28.695][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-06-05 18:21:28.696][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-06-05 18:21:28.697][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-06-05 18:21:28.699][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-06-05 18:21:28.700][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:21:28.702][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-06-05 18:21:28.703][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:21:28.704][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-06-05 18:21:28.706][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:21:28.707][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:21:28.708][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-06-05 18:21:28.710][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:21:28.711][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:21:28.712][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-06-05 18:21:28.714][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:21:28.715][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-06-05 18:21:28.716][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-06-05 18:21:28.718][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-06-05 18:21:28.719][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:21:28.721][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-06-05 18:21:28.722][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:28.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:28.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:28.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:21:28.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:21:28.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:28.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:28.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:28.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:21:28.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:21:28.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:28.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:28.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:28.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:21:28.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:21:28.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:28.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:28.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:28.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:21:28.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:21:28.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:28.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:28.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:28.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:21:28.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:21:28.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:28.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:28.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:28.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:21:28.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:21:28.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:28.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:28.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:28.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:21:28.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:21:28.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:28.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:28.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:28.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:21:28.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:21:28.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:28.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:28.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:28.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:21:28.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:21:28.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:28.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:28.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:28.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:21:28.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:21:28.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:28.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:28.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:28.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:21:28.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:21:28.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:28.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:28.792][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:28.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:21:28.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:21:28.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:28.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:28.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:28.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:21:28.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:21:28.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:28.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:28.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:28.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:21:28.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:21:28.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:28.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:28.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:28.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:21:28.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:21:28.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:28.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:28.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:28.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:21:28.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:21:28.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:28.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:28.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:28.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:21:28.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:21:28.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:28.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:28.829][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-06-05 18:21:28.831][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-06-05 18:21:28.833][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-06-05 18:21:28.835][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-06-05 18:21:28.837][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-06-05 18:21:28.839][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-06-05 18:21:28.841][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-06-05 18:21:28.843][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-06-05 18:21:28.845][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-06-05 18:21:28.847][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-06-05 18:21:28.849][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-06-05 18:21:28.851][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-06-05 18:21:28.853][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-06-05 18:21:28.855][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-06-05 18:21:28.857][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-06-05 18:21:28.859][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-06-05 18:21:28.861][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-06-05 18:21:28.863][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-06-05 18:21:28.881][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-06-05 18:21:28.883][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-06-05 18:21:28.885][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-06-05 18:21:28.887][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-06-05 18:21:28.889][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-06-05 18:21:28.891][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-06-05 18:21:28.893][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-06-05 18:21:28.895][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-06-05 18:21:28.896][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-06-05 18:21:28.898][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-06-05 18:21:28.900][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-06-05 18:21:28.902][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-06-05 18:21:28.904][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-06-05 18:21:28.906][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-06-05 18:21:28.908][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-06-05 18:21:28.910][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-06-05 18:21:28.912][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-06-05 18:21:28.913][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-06-05 18:21:28.915][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-06-05 18:21:28.917][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-06-05 18:21:28.919][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-06-05 18:21:28.921][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-06-05 18:21:28.923][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-06-05 18:21:28.925][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-06-05 18:21:28.927][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-06-05 18:21:28.929][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-06-05 18:21:28.931][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-06-05 18:21:28.932][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-06-05 18:21:28.934][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-06-05 18:21:28.936][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-06-05 18:21:28.938][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-06-05 18:21:28.940][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-06-05 18:21:28.942][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-06-05 18:21:28.944][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-06-05 18:21:28.946][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-06-05 18:21:28.948][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-06-05 18:21:28.949][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-06-05 18:21:28.951][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-06-05 18:21:28.953][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-06-05 18:21:28.955][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-06-05 18:21:28.957][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-06-05 18:21:28.959][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-06-05 18:21:28.961][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-06-05 18:21:28.963][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-06-05 18:21:28.965][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-06-05 18:21:28.967][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-06-05 18:21:28.969][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-06-05 18:21:28.971][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-06-05 18:21:28.973][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-06-05 18:21:28.974][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-06-05 18:21:28.976][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-06-05 18:21:28.978][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-06-05 18:21:28.980][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-06-05 18:21:28.982][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-06-05 18:21:28.984][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-06-05 18:21:28.986][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-06-05 18:21:28.988][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-06-05 18:21:28.989][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-06-05 18:21:28.991][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-06-05 18:21:28.993][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-06-05 18:21:28.995][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-06-05 18:21:28.997][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-06-05 18:21:28.999][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-06-05 18:21:29.001][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-06-05 18:21:29.003][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-06-05 18:21:29.005][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-06-05 18:21:29.007][initialize] This is biodb version 1.9.0.
biodb.DEBUG[2023-06-05 18:21:29.008][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-06-05 18:21:29.009][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:21:29.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:21:29.012][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:29.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:29.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:29.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:21:29.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:21:29.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:21:29.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:21:29.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:29.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:29.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:29.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:21:29.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:21:29.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:21:29.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:21:29.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:29.030][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[2023-06-05 18:21:29.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:29.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:21:29.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:21:29.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:21:29.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:21:29.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:29.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:29.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:29.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:21:29.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:21:29.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:21:29.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:21:29.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:29.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:29.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:29.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:21:29.050][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:21:29.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:21:29.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:21:29.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:29.055][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[2023-06-05 18:21:29.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:29.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:21:29.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:21:29.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:21:29.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:21:29.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:29.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:29.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:29.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:21:29.084][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:21:29.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:21:29.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:21:29.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:29.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:29.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:29.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:21:29.093][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:21:29.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:21:29.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:21:29.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:29.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:29.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:29.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:21:29.101][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:21:29.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:21:29.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:21:29.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:29.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:29.107][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:29.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:21:29.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:21:29.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:21:29.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:21:29.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:29.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:29.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:29.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:21:29.118][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:21:29.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:21:29.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:21:29.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:29.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:29.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:29.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:21:29.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:21:29.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:21:29.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:21:29.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:29.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:29.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:29.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:21:29.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:21:29.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:21:29.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:21:29.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:29.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:29.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:29.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:21:29.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:21:29.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:21:29.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:21:29.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:29.147][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[2023-06-05 18:21:29.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:29.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:21:29.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:21:29.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:21:29.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:21:29.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:29.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:29.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:29.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:21:29.159][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:21:29.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:21:29.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:21:29.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:29.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:29.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:21:29.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:21:29.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:21:29.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:21:29.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:21:29.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:21:29.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:21:29.176][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.0/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-06-05 18:21:29.177][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-06-05 18:21:29.180][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-06-05 18:21:29.181][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-06-05 18:21:29.183][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-06-05 18:21:29.184][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-06-05 18:21:29.185][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-06-05 18:21:29.187][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-06-05 18:21:29.188][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-06-05 18:21:29.189][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-06-05 18:21:29.191][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-06-05 18:21:29.192][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-06-05 18:21:29.193][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-06-05 18:21:29.195][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-06-05 18:21:29.196][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-06-05 18:21:29.197][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-06-05 18:21:29.197][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-06-05 18:21:29.197][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-06-05 18:21:29.197][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-06-05 18:21:29.197][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-06-05 18:21:29.197][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-06-05 18:21:29.197][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-06-05 18:21:29.197][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-06-05 18:21:29.197][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-06-05 18:21:29.199][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-06-05 18:21:29.200][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-06-05 18:21:29.200][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-06-05 18:21:29.202][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-06-05 18:21:29.203][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:21:29.204][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:21:29.205][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-06-05 18:21:29.207][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:21:29.208][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:21:29.209][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-06-05 18:21:29.211][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-06-05 18:21:29.211][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-06-05 18:21:29.212][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-06-05 18:21:29.213][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-06-05 18:21:29.214][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-06-05 18:21:29.216][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:21:29.217][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-06-05 18:21:29.220][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-06-05 18:21:29.224][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-06-05 18:21:29.225][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-06-05 18:21:29.227][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-06-05 18:21:29.229][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-06-05 18:21:29.231][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-06-05 18:21:29.232][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-06-05 18:21:29.234][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-06-05 18:21:29.235][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-06-05 18:21:29.237][biodb::testThat]
biodb.INFO [2023-06-05 18:21:29.238][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2023-06-05 18:21:29.240][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:21:29.241][biodb::testThat]
biodb.DEBUG[2023-06-05 18:21:29.246][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.DEBUG[2023-06-05 18:21:29.252][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-06-05 18:21:29.253][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-06-05 18:21:29.256][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2023-06-05 18:21:30.220][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[2023-06-05 18:21:34.496][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-06-05 18:21:34.505][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2023-06-05 18:21:34.520][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2023-06-05 18:21:34.536][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[2023-06-05 18:21:34.540][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-06-05 18:21:34.542][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-06-05 18:21:34.544][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2023-06-05 18:21:35.486][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty).
biodb.DEBUG[2023-06-05 18:21:36.438][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-06-05 18:21:36.447][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2023-06-05 18:21:36.462][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2023-06-05 18:21:36.476][biodb::testThat]
biodb.INFO [2023-06-05 18:21:36.478][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2023-06-05 18:21:36.492][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:21:36.501][biodb::testThat]
biodb.INFO [2023-06-05 18:21:36.537][biodb::testThat]
biodb.INFO [2023-06-05 18:21:36.539][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2023-06-05 18:21:36.540][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:21:36.542][biodb::testThat]
biodb.DEBUG[2023-06-05 18:21:36.546][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2023-06-05 18:21:36.550][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-06-05 18:21:36.552][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-06-05 18:21:36.554][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2023-06-05 18:21:37.335][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2023-06-05 18:21:38.793][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-06-05 18:21:38.802][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2023-06-05 18:21:38.817][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2023-06-05 18:21:38.826][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[2023-06-05 18:21:38.830][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-06-05 18:21:38.832][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2023-06-05 18:21:38.834][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-06-05 18:21:38.836][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2023-06-05 18:21:38.842][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[2023-06-05 18:21:38.847][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-06-05 18:21:38.848][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-06-05 18:21:38.851][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2023-06-05 18:21:39.622][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2023-06-05 18:21:40.405][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-06-05 18:21:40.415][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2023-06-05 18:21:40.431][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2023-06-05 18:21:40.442][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2023-06-05 18:21:40.446][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-06-05 18:21:40.448][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-06-05 18:21:40.450][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2023-06-05 18:21:41.960][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2023-06-05 18:21:54.937][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-06-05 18:21:54.947][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2023-06-05 18:21:54.965][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2023-06-05 18:21:55.106][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[2023-06-05 18:21:55.111][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-06-05 18:21:55.112][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-06-05 18:21:55.115][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2023-06-05 18:21:56.582][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2023-06-05 18:22:03.684][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-06-05 18:22:03.694][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2023-06-05 18:22:03.713][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2023-06-05 18:22:03.859][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-06-05 18:22:03.861][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-06-05 18:22:03.863][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-06-05 18:22:03.864][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-06-05 18:22:03.865][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:22:03.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:22:03.867][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:03.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:03.870][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:03.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-06-05 18:22:03.876][biodb::testContext]
biodb.INFO [2023-06-05 18:22:03.878][biodb::testContext] ********************************************************************************
biodb.INFO [2023-06-05 18:22:03.879][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2023-06-05 18:22:03.881][biodb::testContext] ********************************************************************************
biodb.INFO [2023-06-05 18:22:03.882][biodb::testContext]
biodb.INFO [2023-06-05 18:22:03.889][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.9.0.
biodb.DEBUG[2023-06-05 18:22:03.891][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.0/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-06-05 18:22:03.896][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-06-05 18:22:03.897][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-06-05 18:22:03.899][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-06-05 18:22:03.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:03.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:03.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:03.904][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-06-05 18:22:03.906][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-06-05 18:22:03.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:03.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:03.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:03.911][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-06-05 18:22:03.912][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-06-05 18:22:03.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:03.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:03.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:03.918][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-06-05 18:22:03.919][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-06-05 18:22:03.921][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-06-05 18:22:03.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:03.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:03.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:03.926][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-06-05 18:22:03.927][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-06-05 18:22:03.929][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-06-05 18:22:03.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:03.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:03.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:03.934][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-06-05 18:22:03.936][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-06-05 18:22:03.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:03.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:03.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:03.941][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-06-05 18:22:03.943][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-06-05 18:22:03.944][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-06-05 18:22:03.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:03.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:03.948][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[2023-06-05 18:22:03.950][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-06-05 18:22:03.951][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-06-05 18:22:03.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:03.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:03.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:03.956][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-06-05 18:22:03.958][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-06-05 18:22:03.959][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-06-05 18:22:03.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:03.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:03.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:03.965][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-06-05 18:22:03.967][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-06-05 18:22:03.968][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-06-05 18:22:03.970][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-06-05 18:22:03.971][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-06-05 18:22:03.973][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-06-05 18:22:03.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:03.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:03.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:03.978][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-06-05 18:22:03.980][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-06-05 18:22:03.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:03.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:03.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:03.985][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-06-05 18:22:03.986][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-06-05 18:22:03.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:03.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:03.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:03.992][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-06-05 18:22:03.993][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-06-05 18:22:03.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:03.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:03.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:03.999][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-06-05 18:22:04.000][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-06-05 18:22:04.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:04.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:04.006][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-06-05 18:22:04.025][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-06-05 18:22:04.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:04.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:04.031][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-06-05 18:22:04.032][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-06-05 18:22:04.037][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-06-05 18:22:04.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:04.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:04.042][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-06-05 18:22:04.044][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-06-05 18:22:04.045][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-06-05 18:22:04.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:04.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:04.051][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-06-05 18:22:04.053][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-06-05 18:22:04.055][self$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[2023-06-05 18:22:04.056][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-06-05 18:22:04.057][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-06-05 18:22:04.059][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-06-05 18:22:04.060][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-06-05 18:22:04.062][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-06-05 18:22:04.063][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-06-05 18:22:04.065][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-06-05 18:22:04.066][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-06-05 18:22:04.068][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-06-05 18:22:04.069][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-06-05 18:22:04.070][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-06-05 18:22:04.072][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:22:04.073][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-06-05 18:22:04.075][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-06-05 18:22:04.075][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-06-05 18:22:04.075][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-06-05 18:22:04.075][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-06-05 18:22:04.075][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-06-05 18:22:04.076][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-06-05 18:22:04.078][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:22:04.079][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:22:04.080][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-06-05 18:22:04.082][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:22:04.083][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:22:04.084][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-06-05 18:22:04.086][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:22:04.087][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-06-05 18:22:04.089][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-06-05 18:22:04.090][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-06-05 18:22:04.091][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:22:04.093][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-06-05 18:22:04.096][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-06-05 18:22:04.097][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-06-05 18:22:04.098][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-06-05 18:22:04.100][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-06-05 18:22:04.101][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-06-05 18:22:04.103][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-06-05 18:22:04.104][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-06-05 18:22:04.106][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-06-05 18:22:04.107][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-06-05 18:22:04.108][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-06-05 18:22:04.110][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-06-05 18:22:04.111][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-06-05 18:22:04.113][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-06-05 18:22:04.114][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:22:04.116][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-06-05 18:22:04.117][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-06-05 18:22:04.117][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-06-05 18:22:04.117][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-06-05 18:22:04.117][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-06-05 18:22:04.117][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-06-05 18:22:04.119][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-06-05 18:22:04.120][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:22:04.121][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:22:04.123][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-06-05 18:22:04.124][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:22:04.125][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:22:04.127][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-06-05 18:22:04.128][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:22:04.130][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-06-05 18:22:04.131][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-06-05 18:22:04.132][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-06-05 18:22:04.134][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:22:04.135][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-06-05 18:22:04.138][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-06-05 18:22:04.139][self$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[2023-06-05 18:22:04.141][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-06-05 18:22:04.142][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-06-05 18:22:04.144][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-06-05 18:22:04.145][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-06-05 18:22:04.147][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-06-05 18:22:04.148][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-06-05 18:22:04.150][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-06-05 18:22:04.151][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-06-05 18:22:04.153][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-06-05 18:22:04.154][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-06-05 18:22:04.155][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-06-05 18:22:04.157][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:22:04.158][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-06-05 18:22:04.160][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:22:04.161][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-06-05 18:22:04.162][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:22:04.164][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:22:04.165][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-06-05 18:22:04.167][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:22:04.168][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:22:04.170][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-06-05 18:22:04.171][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:22:04.172][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-06-05 18:22:04.174][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-06-05 18:22:04.175][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-06-05 18:22:04.176][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:22:04.178][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-06-05 18:22:04.181][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-06-05 18:22:04.182][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-06-05 18:22:04.183][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-06-05 18:22:04.185][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-06-05 18:22:04.186][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-06-05 18:22:04.188][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-06-05 18:22:04.189][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-06-05 18:22:04.190][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-06-05 18:22:04.192][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-06-05 18:22:04.193][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-06-05 18:22:04.195][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-06-05 18:22:04.196][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-06-05 18:22:04.198][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-06-05 18:22:04.199][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:22:04.201][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-06-05 18:22:04.202][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:22:04.203][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-06-05 18:22:04.205][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:22:04.206][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:22:04.207][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-06-05 18:22:04.209][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:22:04.210][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:22:04.212][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-06-05 18:22:04.213][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:22:04.214][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-06-05 18:22:04.216][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-06-05 18:22:04.217][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-06-05 18:22:04.219][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:22:04.221][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-06-05 18:22:04.222][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.223][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[2023-06-05 18:22:04.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:04.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:04.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:04.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:04.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:04.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:04.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:04.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:04.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:04.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:04.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:04.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:04.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:04.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:04.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:04.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:04.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:04.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:04.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:04.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:04.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:04.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:04.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:04.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:04.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:04.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:04.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:04.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:04.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:04.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:04.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:04.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:04.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:04.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:04.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:04.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:04.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:04.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:04.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:04.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.301][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[2023-06-05 18:22:04.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:04.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:04.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:04.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:04.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:04.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:04.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:04.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:04.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:04.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:04.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:04.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:04.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:04.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:04.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:04.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:04.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:04.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:04.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:04.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:04.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:04.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:04.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:04.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:04.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:04.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:04.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:04.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:04.346][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-06-05 18:22:04.348][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-06-05 18:22:04.350][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-06-05 18:22:04.352][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-06-05 18:22:04.354][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-06-05 18:22:04.356][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-06-05 18:22:04.358][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-06-05 18:22:04.360][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-06-05 18:22:04.361][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-06-05 18:22:04.363][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-06-05 18:22:04.365][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-06-05 18:22:04.367][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-06-05 18:22:04.369][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-06-05 18:22:04.372][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-06-05 18:22:04.374][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-06-05 18:22:04.376][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-06-05 18:22:04.377][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-06-05 18:22:04.379][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-06-05 18:22:04.381][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-06-05 18:22:04.383][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-06-05 18:22:04.385][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-06-05 18:22:04.387][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-06-05 18:22:04.389][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-06-05 18:22:04.391][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-06-05 18:22:04.393][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-06-05 18:22:04.395][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-06-05 18:22:04.397][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-06-05 18:22:04.399][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-06-05 18:22:04.401][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-06-05 18:22:04.403][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-06-05 18:22:04.405][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-06-05 18:22:04.407][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-06-05 18:22:04.409][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-06-05 18:22:04.411][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-06-05 18:22:04.413][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-06-05 18:22:04.415][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-06-05 18:22:04.417][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-06-05 18:22:04.419][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-06-05 18:22:04.421][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-06-05 18:22:04.423][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-06-05 18:22:04.425][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-06-05 18:22:04.427][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-06-05 18:22:04.429][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-06-05 18:22:04.431][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-06-05 18:22:04.433][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-06-05 18:22:04.435][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-06-05 18:22:04.451][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-06-05 18:22:04.453][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-06-05 18:22:04.455][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-06-05 18:22:04.457][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-06-05 18:22:04.459][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-06-05 18:22:04.461][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-06-05 18:22:04.463][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-06-05 18:22:04.465][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-06-05 18:22:04.467][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-06-05 18:22:04.469][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-06-05 18:22:04.471][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-06-05 18:22:04.473][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-06-05 18:22:04.475][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-06-05 18:22:04.477][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-06-05 18:22:04.479][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-06-05 18:22:04.481][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-06-05 18:22:04.483][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-06-05 18:22:04.485][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-06-05 18:22:04.486][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-06-05 18:22:04.488][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-06-05 18:22:04.490][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-06-05 18:22:04.492][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-06-05 18:22:04.494][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-06-05 18:22:04.496][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-06-05 18:22:04.498][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-06-05 18:22:04.500][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-06-05 18:22:04.502][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-06-05 18:22:04.504][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-06-05 18:22:04.506][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-06-05 18:22:04.508][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-06-05 18:22:04.510][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-06-05 18:22:04.512][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-06-05 18:22:04.514][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-06-05 18:22:04.515][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-06-05 18:22:04.517][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-06-05 18:22:04.519][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-06-05 18:22:04.521][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-06-05 18:22:04.523][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-06-05 18:22:04.525][initialize] This is biodb version 1.9.0.
biodb.DEBUG[2023-06-05 18:22:04.527][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-06-05 18:22:04.528][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:04.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:04.530][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:04.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:04.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:22:04.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:22:04.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:04.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:04.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:04.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:04.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:22:04.544][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:22:04.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:04.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:04.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:04.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:04.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:22:04.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:22:04.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:04.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:04.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:04.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:04.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:22:04.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:22:04.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:04.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:04.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:04.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:04.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:22:04.570][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:22:04.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:04.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:04.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:04.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:04.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:22:04.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:22:04.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:04.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:04.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:04.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:04.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:22:04.588][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:22:04.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:04.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:04.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:04.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:04.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:22:04.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:22:04.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:04.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:04.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:04.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:04.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:22:04.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:22:04.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:04.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:04.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:04.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:04.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:22:04.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:22:04.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:04.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:04.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:04.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:04.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:22:04.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:22:04.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:04.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:04.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:04.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:04.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:22:04.632][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:22:04.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:04.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:04.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.637][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[2023-06-05 18:22:04.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:04.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:22:04.655][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:22:04.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:04.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:04.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:04.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:04.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:22:04.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:22:04.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:04.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:04.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:04.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:04.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:22:04.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:22:04.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:04.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:04.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:04.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:04.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:22:04.681][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:22:04.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:04.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:04.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:04.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-06-05 18:22:04.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:22:04.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:22:04.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:04.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:04.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:04.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-06-05 18:22:04.696][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.0/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-06-05 18:22:04.698][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-06-05 18:22:04.700][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-06-05 18:22:04.702][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-06-05 18:22:04.703][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-06-05 18:22:04.704][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-06-05 18:22:04.706][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-06-05 18:22:04.707][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-06-05 18:22:04.708][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-06-05 18:22:04.710][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-06-05 18:22:04.711][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-06-05 18:22:04.713][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-06-05 18:22:04.714][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-06-05 18:22:04.715][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-06-05 18:22:04.717][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-06-05 18:22:04.718][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-06-05 18:22:04.718][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-06-05 18:22:04.718][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-06-05 18:22:04.718][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-06-05 18:22:04.718][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-06-05 18:22:04.718][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-06-05 18:22:04.718][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-06-05 18:22:04.718][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-06-05 18:22:04.718][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-06-05 18:22:04.719][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-06-05 18:22:04.721][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-06-05 18:22:04.721][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-06-05 18:22:04.722][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-06-05 18:22:04.723][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:22:04.725][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:22:04.726][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-06-05 18:22:04.727][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-06-05 18:22:04.729][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-06-05 18:22:04.730][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-06-05 18:22:04.731][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-06-05 18:22:04.731][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-06-05 18:22:04.733][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-06-05 18:22:04.734][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-06-05 18:22:04.735][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-06-05 18:22:04.736][self$setPropertyValue]
biodb.DEBUG[2023-06-05 18:22:04.738][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-06-05 18:22:04.740][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-06-05 18:22:04.744][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-06-05 18:22:04.745][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-06-05 18:22:04.747][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-06-05 18:22:04.749][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-06-05 18:22:04.751][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-06-05 18:22:04.752][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-06-05 18:22:04.754][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-06-05 18:22:04.755][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-06-05 18:22:04.757][biodb::testThat]
biodb.INFO [2023-06-05 18:22:04.758][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2023-06-05 18:22:04.760][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-06-05 18:22:04.761][biodb::testThat]
biodb.DEBUG[2023-06-05 18:22:04.766][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2023-06-05 18:22:04.771][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-06-05 18:22:04.773][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2023-06-05 18:22:04.775][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-06-05 18:22:04.861][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2023-06-05 18:22:05.893][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2023-06-05 18:22:05.894][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-06-05 18:22:05.896][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2023-06-05 18:22:05.898][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2023-06-05 18:22:05.900][loadFileContents] Loaded 2 files from cache: [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2023-06-05 18:22:05.902][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-06-05 18:22:05.924][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-06-05 18:22:05.925][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-06-05 18:22:05.928][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:22:05.929][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:22:05.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:22:05.938][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:05.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:05.940][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:05.941][FUN] Functions in observer BiodbConfig: [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[2023-06-05 18:22:05.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:22:05.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:22:05.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:05.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:05.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:22:05.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:22:05.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:05.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:05.963][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:22:05.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:22:05.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:05.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:05.969][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:22:05.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:22:05.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:05.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:05.978][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:22:05.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:22:05.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:05.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:05.984][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:22:05.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:22:05.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:05.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:05.989][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:22:05.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:22:05.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:05.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:05.996][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:22:05.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:22:05.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.006][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:22:06.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:22:06.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.011][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:22:06.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:22:06.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.021][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-06-05 18:22:06.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:22:06.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.026][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-06-05 18:22:06.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:22:06.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.036][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:22:06.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:22:06.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.041][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:22:06.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:22:06.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.050][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:22:06.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:22:06.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.056][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:22:06.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:22:06.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.065][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-06-05 18:22:06.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:22:06.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.071][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-06-05 18:22:06.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:22:06.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.077][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:22:06.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:22:06.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.104][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:22:06.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:22:06.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.110][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-06-05 18:22:06.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:22:06.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.119][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:22:06.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:22:06.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.125][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:22:06.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:22:06.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.130][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:22:06.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:22:06.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.136][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:22:06.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:22:06.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.141][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:22:06.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:22:06.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.151][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:22:06.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:22:06.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.156][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:22:06.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:22:06.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:22:06.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:22:06.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.167][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:22:06.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:22:06.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:22:06.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:22:06.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:22:06.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:22:06.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.183][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:22:06.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:22:06.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:22:06.193][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:22:06.194][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:22:06.195][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:22:06.203][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:06.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:06.205][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:06.207][FUN] Functions in observer BiodbConfig: [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[2023-06-05 18:22:06.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:22:06.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:22:06.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:22:06.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:22:06.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.229][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:22:06.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:22:06.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.234][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:22:06.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:22:06.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.244][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:22:06.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-06-05 18:22:06.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.250][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:22:06.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-06-05 18:22:06.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.255][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:22:06.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:22:06.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.261][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:22:06.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:22:06.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.270][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:22:06.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:22:06.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.276][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:22:06.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:22:06.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.285][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-06-05 18:22:06.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:22:06.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.308][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-06-05 18:22:06.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:22:06.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.317][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:22:06.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:22:06.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.323][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:22:06.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:22:06.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.333][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:22:06.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:22:06.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.339][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:22:06.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:22:06.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.348][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-06-05 18:22:06.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:22:06.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.354][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-06-05 18:22:06.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:22:06.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.360][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:22:06.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:22:06.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.365][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:22:06.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:22:06.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.371][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-06-05 18:22:06.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:22:06.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.380][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:22:06.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:22:06.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.386][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:22:06.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:22:06.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:22:06.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:22:06.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.398][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:22:06.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:22:06.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:22:06.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:22:06.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:22:06.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:22:06.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:22:06.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:22:06.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:22:06.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:22:06.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:22:06.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:22:06.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:22:06.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:22:06.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:22:06.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:22:06.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:22:06.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:22:06.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:22:06.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:22:06.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-06-05 18:22:06.460][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2023-06-05 18:22:06.463][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-06-05 18:22:06.465][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:22:06.466][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:22:06.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:22:06.475][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:06.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:06.478][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:06.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-06-05 18:22:06.482][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-06-05 18:22:06.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-06-05 18:22:06.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.488][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-06-05 18:22:06.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-06-05 18:22:06.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.494][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-06-05 18:22:06.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-06-05 18:22:06.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.516][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-06-05 18:22:06.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-06-05 18:22:06.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.522][private$selectFields] Fields none
biodb.TRACE[2023-06-05 18:22:06.523][private$selectFields]
biodb.TRACE[2023-06-05 18:22:06.524][private$selectFields] Fields is null: TRUE
biodb.TRACE[2023-06-05 18:22:06.526][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-06-05 18:22:06.527][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:22:06.528][ef$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:22:06.530][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:22:06.531][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.533][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.534][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:22:06.535][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:22:06.537][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.538][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.539][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:22:06.541][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:22:06.542][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.543][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.545][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:22:06.546][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:22:06.548][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.549][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.550][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:22:06.552][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:22:06.553][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.554][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.556][ef$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:22:06.557][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:22:06.558][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.560][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.561][ef$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:22:06.563][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:22:06.564][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.565][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.567][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:22:06.568][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:22:06.569][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.571][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.572][ef$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:22:06.574][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:22:06.575][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.576][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.578][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:22:06.579][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:22:06.580][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.582][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.583][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:22:06.585][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:22:06.586][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.587][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.589][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:22:06.590][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:22:06.592][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.593][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.594][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:22:06.596][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:22:06.597][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.598][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.600][ef$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:22:06.601][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:22:06.603][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.604][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.605][ef$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:22:06.607][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:22:06.608][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.609][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.611][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:22:06.614][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:22:06.615][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.616][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.618][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:22:06.619][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:22:06.620][ef$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:22:06.622][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:22:06.623][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.624][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.626][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:22:06.627][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:22:06.629][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.630][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.631][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:22:06.633][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:22:06.634][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.635][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.637][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:22:06.638][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:22:06.639][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.641][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.642][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:22:06.644][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:22:06.645][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.646][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.647][ef$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:22:06.649][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:22:06.650][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.651][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.653][ef$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:22:06.654][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:22:06.656][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.657][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.658][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:22:06.660][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:22:06.661][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.662][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.664][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2023-06-05 18:22:06.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:22:06.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:22:06.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:22:06.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:22:06.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:22:06.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:22:06.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.682][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:22:06.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:22:06.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.687][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:22:06.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:22:06.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.693][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:22:06.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:22:06.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.699][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:22:06.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:22:06.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.721][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:22:06.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:22:06.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.726][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:22:06.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:22:06.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.732][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:22:06.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:22:06.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.737][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:22:06.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:22:06.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.743][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:22:06.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:22:06.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.748][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:22:06.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:22:06.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.753][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:22:06.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:22:06.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.759][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:22:06.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:22:06.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.764][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:22:06.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:22:06.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.770][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:22:06.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:22:06.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.775][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:22:06.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:22:06.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.781][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:22:06.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:22:06.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.786][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:22:06.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:22:06.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.792][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:22:06.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:22:06.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.797][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:22:06.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:22:06.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.803][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:22:06.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:22:06.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.808][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:22:06.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:22:06.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.823][private$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[2023-06-05 18:22:06.825][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-06-05 18:22:06.826][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:22:06.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:22:06.835][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:06.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:06.837][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:06.838][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.TRACE[2023-06-05 18:22:06.841][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-06-05 18:22:06.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-06-05 18:22:06.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.847][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-06-05 18:22:06.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-06-05 18:22:06.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.852][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-06-05 18:22:06.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-06-05 18:22:06.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.858][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-06-05 18:22:06.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-06-05 18:22:06.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.863][private$selectFields] Fields none
biodb.TRACE[2023-06-05 18:22:06.864][private$selectFields]
biodb.TRACE[2023-06-05 18:22:06.866][private$selectFields] Fields is null: TRUE
biodb.TRACE[2023-06-05 18:22:06.867][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-06-05 18:22:06.868][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:22:06.870][ef$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:22:06.871][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:22:06.872][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.874][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.875][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:22:06.877][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:22:06.878][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.879][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.880][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:22:06.882][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:22:06.883][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.885][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.886][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:22:06.887][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:22:06.889][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.890][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.891][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:22:06.893][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:22:06.894][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.896][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.897][ef$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:22:06.915][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:22:06.917][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.918][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.919][ef$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:22:06.921][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:22:06.922][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.923][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.925][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:22:06.926][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:22:06.927][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.929][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.930][ef$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:22:06.932][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:22:06.933][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.934][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.935][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:22:06.937][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:22:06.938][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.939][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.941][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:22:06.942][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:22:06.944][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.945][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.946][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:22:06.948][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:22:06.949][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.950][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.952][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:22:06.953][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:22:06.954][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.956][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.957][ef$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:22:06.958][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:22:06.960][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.961][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.962][ef$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:22:06.964][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:22:06.965][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.967][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.968][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:22:06.970][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:22:06.971][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.972][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.974][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:22:06.975][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-06-05 18:22:06.976][ef$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:22:06.978][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:22:06.979][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.980][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.982][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:22:06.983][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:22:06.984][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.986][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.987][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:22:06.988][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:22:06.990][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.991][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.992][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:22:06.994][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:22:06.995][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:06.996][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:06.998][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:22:06.999][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:22:07.001][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:07.002][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:07.003][ef$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:22:07.005][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:22:07.006][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:07.007][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:07.009][ef$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:22:07.010][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:22:07.011][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:07.013][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:07.014][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:22:07.016][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:22:07.018][ef$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:07.019][ef$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:07.021][private$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[2023-06-05 18:22:07.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:22:07.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:22:07.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:07.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:07.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:22:07.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:22:07.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:07.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:07.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-06-05 18:22:07.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-06-05 18:22:07.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:07.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:07.038][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:22:07.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:22:07.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:07.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:07.044][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:22:07.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:22:07.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:07.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:07.049][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-06-05 18:22:07.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-06-05 18:22:07.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:07.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:07.055][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:22:07.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:22:07.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:07.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:07.060][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:22:07.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:22:07.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:07.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:07.066][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:22:07.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-06-05 18:22:07.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:07.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:07.071][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:22:07.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:22:07.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:07.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:07.077][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:22:07.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:22:07.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:07.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:07.082][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:22:07.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-06-05 18:22:07.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:07.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:07.088][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:22:07.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:22:07.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:07.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:07.094][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:22:07.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:22:07.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:07.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:07.116][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:22:07.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-06-05 18:22:07.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:07.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:07.122][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:22:07.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:22:07.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:07.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:07.127][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:22:07.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:22:07.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:07.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:07.132][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-06-05 18:22:07.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-06-05 18:22:07.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:07.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:07.137][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:22:07.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:22:07.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:07.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:07.143][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:22:07.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:22:07.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:07.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:07.148][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-06-05 18:22:07.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-06-05 18:22:07.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:07.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:07.153][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:22:07.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:22:07.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:07.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:07.159][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:22:07.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:22:07.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:07.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:07.164][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:22:07.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-06-05 18:22:07.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-06-05 18:22:07.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-06-05 18:22:07.175][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000002, 137783, 42607281, N-(3S-hydroxydecanoyl)-L-serine, 275.173274, ...].
biodb.DEBUG[2023-06-05 18:22:07.176][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-06-05 18:22:07.177][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2023-06-05 18:22:07.181][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-06-05 18:22:07.183][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-06-05 18:22:07.184][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-06-05 18:22:07.186][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-06-05 18:22:07.187][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-06-05 18:22:07.188][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-06-05 18:22:07.189][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-06-05 18:22:07.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-06-05 18:22:07.192][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-06-05 18:22:07.193][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 168 ]
> 
> proc.time()
   user  system elapsed 
 26.581   1.450 250.442

Example timings

biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings

nameusersystemelapsed
LipidmapsStructureConn1.2920.0794.169
LipidmapsStructureEntry0.2540.0010.256