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This page was generated on 2023-10-16 11:35:13 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 199/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbLipidmaps 1.6.0  (landing page)
Pierrick Roger
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/biodbLipidmaps
git_branch: RELEASE_3_17
git_last_commit: 3555696
git_last_commit_date: 2023-04-25 11:34:40 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for biodbLipidmaps on nebbiolo1


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

raw results

Summary

Package: biodbLipidmaps
Version: 1.6.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings biodbLipidmaps_1.6.0.tar.gz
StartedAt: 2023-10-15 19:35:59 -0400 (Sun, 15 Oct 2023)
EndedAt: 2023-10-15 19:39:16 -0400 (Sun, 15 Oct 2023)
EllapsedTime: 197.6 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbLipidmaps.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings biodbLipidmaps_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/biodbLipidmaps.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘biodbLipidmaps/DESCRIPTION’ ... OK
* this is package ‘biodbLipidmaps’ version ‘1.6.0’
* 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/bbs-3.17-bioc/R/bin/R CMD INSTALL biodbLipidmaps
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘biodbLipidmaps’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** 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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 [2023-10-15 19:36:43.196][biodb::testContext]
biodb.INFO [2023-10-15 19:36:43.201][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-15 19:36:43.202][biodb::testContext] Test context - Generic tests
biodb.INFO [2023-10-15 19:36:43.203][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-15 19:36:43.204][biodb::testContext]
biodb.INFO [2023-10-15 19:36:43.216][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.8.1.
biodb.DEBUG[2023-10-15 19:36:43.219][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-10-15 19:36:43.229][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-15 19:36:43.231][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-10-15 19:36:43.232][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-10-15 19:36:43.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.236][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-10-15 19:36:43.258][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-10-15 19:36:43.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.263][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-10-15 19:36:43.264][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-10-15 19:36:43.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.268][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-10-15 19:36:43.269][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-10-15 19:36:43.270][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-10-15 19:36:43.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.274][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-10-15 19:36:43.275][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-10-15 19:36:43.276][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-10-15 19:36:43.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.280][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-10-15 19:36:43.281][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-10-15 19:36:43.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.285][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-10-15 19:36:43.286][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-10-15 19:36:43.287][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-10-15 19:36:43.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.291][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-10-15 19:36:43.292][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-10-15 19:36:43.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.295][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[2023-10-15 19:36:43.296][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-10-15 19:36:43.297][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-10-15 19:36:43.298][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-10-15 19:36:43.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.302][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-10-15 19:36:43.303][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-10-15 19:36:43.304][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-10-15 19:36:43.305][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-10-15 19:36:43.307][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-10-15 19:36:43.308][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-10-15 19:36:43.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.312][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-10-15 19:36:43.313][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-10-15 19:36:43.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.317][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-10-15 19:36:43.318][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-10-15 19:36:43.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.320][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[2023-10-15 19:36:43.321][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-10-15 19:36:43.323][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-10-15 19:36:43.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.326][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-10-15 19:36:43.328][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-10-15 19:36:43.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.331][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-10-15 19:36:43.333][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-10-15 19:36:43.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.336][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-10-15 19:36:43.337][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-10-15 19:36:43.341][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-10-15 19:36:43.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.344][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[2023-10-15 19:36:43.345][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-10-15 19:36:43.347][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-10-15 19:36:43.348][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-10-15 19:36:43.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.355][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-10-15 19:36:43.393][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-15 19:36:43.411][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-10-15 19:36:43.412][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-15 19:36:43.414][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-15 19:36:43.415][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-15 19:36:43.416][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-15 19:36:43.417][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-15 19:36:43.418][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-15 19:36:43.419][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-15 19:36:43.420][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-15 19:36:43.421][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-15 19:36:43.457][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-10-15 19:36:43.459][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-15 19:36:43.460][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:36:43.461][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-15 19:36:43.463][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-15 19:36:43.463][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-15 19:36:43.463][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-15 19:36:43.463][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-15 19:36:43.463][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-15 19:36:43.464][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-15 19:36:43.465][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 19:36:43.467][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 19:36:43.468][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-15 19:36:43.470][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 19:36:43.471][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 19:36:43.472][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-15 19:36:43.474][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:36:43.475][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-15 19:36:43.476][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-15 19:36:43.478][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-15 19:36:43.480][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:36:43.481][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-10-15 19:36:43.484][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-15 19:36:43.485][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-10-15 19:36:43.486][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-15 19:36:43.488][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-15 19:36:43.489][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-15 19:36:43.490][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-15 19:36:43.491][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-15 19:36:43.493][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-15 19:36:43.494][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-15 19:36:43.495][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-15 19:36:43.497][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-15 19:36:43.498][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-10-15 19:36:43.499][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-15 19:36:43.501][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:36:43.502][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-15 19:36:43.504][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-15 19:36:43.504][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-15 19:36:43.504][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-15 19:36:43.504][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-15 19:36:43.504][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-15 19:36:43.505][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-15 19:36:43.507][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 19:36:43.508][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 19:36:43.509][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-15 19:36:43.511][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 19:36:43.512][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 19:36:43.513][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-15 19:36:43.515][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:36:43.517][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-15 19:36:43.518][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-15 19:36:43.519][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-15 19:36:43.520][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:36:43.522][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-10-15 19:36:43.524][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-15 19:36:43.525][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-10-15 19:36:43.526][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-15 19:36:43.527][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-15 19:36:43.528][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-15 19:36:43.529][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-15 19:36:43.530][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-15 19:36:43.531][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-15 19:36:43.532][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-15 19:36:43.533][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-15 19:36:43.534][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-15 19:36:43.536][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-10-15 19:36:43.537][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-15 19:36:43.537][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:36:43.538][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-15 19:36:43.539][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:36:43.540][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-15 19:36:43.541][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 19:36:43.542][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 19:36:43.543][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-15 19:36:43.544][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 19:36:43.545][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 19:36:43.546][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-15 19:36:43.547][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:36:43.548][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-15 19:36:43.549][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-15 19:36:43.550][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-15 19:36:43.551][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:36:43.552][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-10-15 19:36:43.554][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-15 19:36:43.555][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-10-15 19:36:43.555][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-15 19:36:43.556][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-15 19:36:43.557][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-15 19:36:43.558][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-15 19:36:43.559][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-15 19:36:43.560][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-15 19:36:43.561][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-15 19:36:43.562][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-15 19:36:43.563][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-15 19:36:43.564][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-10-15 19:36:43.565][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-15 19:36:43.566][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:36:43.567][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-15 19:36:43.568][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:36:43.569][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-15 19:36:43.570][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 19:36:43.571][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 19:36:43.571][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-15 19:36:43.572][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 19:36:43.573][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 19:36:43.574][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-15 19:36:43.575][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:36:43.576][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-15 19:36:43.577][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-15 19:36:43.578][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-15 19:36:43.579][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:36:43.583][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-15 19:36:43.584][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:36:43.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:36:43.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:36:43.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:36:43.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:36:43.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:36:43.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:36:43.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:36:43.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.602][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[2023-10-15 19:36:43.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:36:43.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:36:43.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:36:43.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:36:43.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:36:43.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:36:43.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:36:43.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:36:43.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:36:43.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:36:43.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:36:43.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:36:43.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:36:43.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:36:43.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:36:43.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:36:43.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:36:43.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:36:43.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:36:43.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:36:43.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:36:43.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:36:43.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:36:43.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:36:43.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:36:43.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:36:43.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.660][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-10-15 19:36:43.665][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-10-15 19:36:43.666][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-10-15 19:36:43.668][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-10-15 19:36:43.669][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-10-15 19:36:43.670][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-10-15 19:36:43.672][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-10-15 19:36:43.673][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-10-15 19:36:43.674][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-10-15 19:36:43.676][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-10-15 19:36:43.677][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-10-15 19:36:43.678][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-10-15 19:36:43.680][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-10-15 19:36:43.681][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-10-15 19:36:43.682][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-10-15 19:36:43.683][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-10-15 19:36:43.685][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-10-15 19:36:43.686][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-10-15 19:36:43.687][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-10-15 19:36:43.689][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-10-15 19:36:43.690][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-10-15 19:36:43.691][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-10-15 19:36:43.693][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-10-15 19:36:43.694][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-10-15 19:36:43.695][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-10-15 19:36:43.697][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-10-15 19:36:43.698][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-10-15 19:36:43.699][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-10-15 19:36:43.701][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-10-15 19:36:43.702][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-10-15 19:36:43.703][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-10-15 19:36:43.705][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-10-15 19:36:43.706][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-10-15 19:36:43.707][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-10-15 19:36:43.709][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-10-15 19:36:43.710][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-10-15 19:36:43.711][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-10-15 19:36:43.713][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-10-15 19:36:43.714][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-10-15 19:36:43.715][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-10-15 19:36:43.717][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-10-15 19:36:43.718][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-10-15 19:36:43.719][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-10-15 19:36:43.721][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-10-15 19:36:43.722][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-10-15 19:36:43.723][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-10-15 19:36:43.725][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-10-15 19:36:43.726][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-10-15 19:36:43.727][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-10-15 19:36:43.729][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-10-15 19:36:43.730][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-10-15 19:36:43.732][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-10-15 19:36:43.738][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-10-15 19:36:43.739][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-10-15 19:36:43.741][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-10-15 19:36:43.742][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-10-15 19:36:43.743][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-10-15 19:36:43.745][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-10-15 19:36:43.746][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-10-15 19:36:43.747][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-10-15 19:36:43.748][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-10-15 19:36:43.750][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-10-15 19:36:43.751][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-10-15 19:36:43.752][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-10-15 19:36:43.754][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-10-15 19:36:43.755][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-10-15 19:36:43.756][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-10-15 19:36:43.758][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-10-15 19:36:43.759][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-10-15 19:36:43.760][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-10-15 19:36:43.761][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-10-15 19:36:43.763][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-10-15 19:36:43.764][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-10-15 19:36:43.765][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-10-15 19:36:43.767][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-10-15 19:36:43.768][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-10-15 19:36:43.769][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-10-15 19:36:43.770][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-10-15 19:36:43.772][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-10-15 19:36:43.773][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-10-15 19:36:43.775][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-10-15 19:36:43.776][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-10-15 19:36:43.777][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-10-15 19:36:43.783][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-10-15 19:36:43.785][initialize] This is biodb version 1.8.1.
biodb.DEBUG[2023-10-15 19:36:43.788][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-15 19:36:43.789][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:36:43.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:36:43.791][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:36:43.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:36:43.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:36:43.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:36:43.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:36:43.804][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:36:43.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:36:43.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:36:43.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:36:43.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:36:43.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:36:43.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:36:43.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:36:43.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:36:43.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:36:43.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:36:43.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:36:43.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:36:43.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:36:43.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:36:43.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.825][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[2023-10-15 19:36:43.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:36:43.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:36:43.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:36:43.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:36:43.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.831][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[2023-10-15 19:36:43.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:36:43.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:36:43.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:36:43.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:36:43.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:36:43.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:36:43.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:36:43.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:36:43.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:36:43.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:36:43.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:36:43.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:36:43.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:36:43.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:36:43.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:36:43.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:36:43.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:36:43.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:36:43.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:36:43.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:36:43.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:36:43.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:36:43.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:36:43.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:36:43.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:36:43.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:36:43.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:36:43.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:36:43.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:36:43.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:36:43.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:36:43.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:36:43.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:36:43.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:36:43.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:36:43.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:36:43.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:36:43.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:36:43.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:36:43.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:36:43.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:36:43.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:36:43.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:36:43.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:36:43.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:36:43.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:43.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:36:43.899][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-10-15 19:36:43.908][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-10-15 19:36:43.910][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-15 19:36:43.911][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-10-15 19:36:43.912][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-15 19:36:43.913][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-15 19:36:43.914][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-15 19:36:43.915][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-15 19:36:43.916][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-10-15 19:36:43.917][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-15 19:36:43.918][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-15 19:36:43.919][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-15 19:36:43.920][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-15 19:36:43.921][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-10-15 19:36:43.922][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-15 19:36:43.923][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-10-15 19:36:43.923][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-10-15 19:36:43.923][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-10-15 19:36:43.923][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-10-15 19:36:43.923][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-10-15 19:36:43.923][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-10-15 19:36:43.923][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-10-15 19:36:43.923][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-10-15 19:36:43.923][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-10-15 19:36:43.924][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-10-15 19:36:43.925][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-15 19:36:43.925][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-15 19:36:43.926][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-15 19:36:43.927][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 19:36:43.928][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 19:36:43.928][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-15 19:36:43.929][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 19:36:43.930][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 19:36:43.931][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-15 19:36:43.932][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-10-15 19:36:43.932][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-10-15 19:36:43.933][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-15 19:36:43.934][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-15 19:36:43.935][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-10-15 19:36:43.936][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:36:43.942][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-10-15 19:36:43.943][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-10-15 19:36:43.969][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-10-15 19:36:43.971][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-10-15 19:36:43.975][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-10-15 19:36:43.980][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-10-15 19:36:43.985][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-10-15 19:36:43.986][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-10-15 19:36:43.988][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-10-15 19:36:43.989][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-10-15 19:36:43.999][biodb::testThat]
biodb.INFO [2023-10-15 19:36:44.001][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2023-10-15 19:36:44.001][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 19:36:44.002][biodb::testThat]
biodb.TRACE[2023-10-15 19:36:44.007][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2023-10-15 19:36:44.016][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-10-15 19:36:44.020][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-10-15 19:36:44.028][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 19:36:44.029][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:36:44.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:36:44.045][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:36:44.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:36:44.047][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:44.047][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.TRACE[2023-10-15 19:36:44.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:36:44.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:36:44.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:36:44.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:36:44.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.079][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 19:36:44.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 19:36:44.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.083][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-10-15 19:36:44.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-10-15 19:36:44.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.087][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-15 19:36:44.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-15 19:36:44.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.091][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:36:44.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:36:44.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.118][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:36:44.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:36:44.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.122][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:36:44.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:36:44.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.126][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:36:44.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:36:44.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.130][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-15 19:36:44.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:36:44.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.134][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-15 19:36:44.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:36:44.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.138][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 19:36:44.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 19:36:44.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.142][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 19:36:44.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 19:36:44.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.146][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:36:44.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:44.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.150][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:36:44.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:44.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.154][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-15 19:36:44.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:44.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.158][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-10-15 19:36:44.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:44.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.161][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:36:44.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:44.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.165][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:36:44.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:44.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.169][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-15 19:36:44.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:44.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.189][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:36:44.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:44.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.193][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:36:44.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:44.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.227][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:36:44.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:44.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.231][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:36:44.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:44.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.242][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:36:44.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:44.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.246][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:36:44.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:36:44.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.250][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:36:44.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:36:44.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:36:44.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:36:44.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.257][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:36:44.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:36:44.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:36:44.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:36:44.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.265][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:36:44.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:36:44.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:36:44.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:36:44.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:36:44.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:36:44.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.276][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:36:44.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:36:44.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:36:44.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:36:44.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-15 19:36:44.284][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2023-10-15 19:36:44.286][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-15 19:36:44.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-15 19:36:44.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.290][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-15 19:36:44.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-15 19:36:44.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.294][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-10-15 19:36:44.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-10-15 19:36:44.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.298][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-10-15 19:36:44.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-10-15 19:36:44.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:36:44.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:36:44.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.335][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:36:44.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:36:44.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:36:44.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:36:44.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:36:44.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:36:44.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.352][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:36:44.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:36:44.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:36:44.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:36:44.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:36:44.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:36:44.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:36:44.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:36:44.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.369][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:36:44.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:36:44.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.373][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:36:44.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:36:44.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.377][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:36:44.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:36:44.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:36:44.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:36:44.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.394][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:36:44.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:36:44.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:36:44.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:36:44.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.402][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:36:44.403][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:36:44.404][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.404][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:36:44.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:36:44.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.418][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:36:44.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:44.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.422][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:36:44.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:44.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.426][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:36:44.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:44.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.430][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:36:44.431][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:44.432][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.433][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.434][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:36:44.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:44.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.447][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:36:44.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:36:44.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.451][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:36:44.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:36:44.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.455][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:36:44.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:36:44.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.459][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:36:44.461][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:36:44.462][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.462][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.464][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:36:44.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:36:44.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.483][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 19:36:44.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 19:36:44.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.488][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 19:36:44.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 19:36:44.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.492][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 19:36:44.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 19:36:44.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.496][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 19:36:44.497][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 19:36:44.498][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.499][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.500][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 19:36:44.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 19:36:44.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.514][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:36:44.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:36:44.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.518][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:36:44.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:36:44.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.522][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:36:44.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:36:44.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.526][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:36:44.527][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:36:44.528][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.529][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.530][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:36:44.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:36:44.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.544][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:36:44.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:36:44.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.548][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:36:44.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:36:44.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.553][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:36:44.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:36:44.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.557][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:36:44.558][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:36:44.559][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.560][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.561][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:36:44.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:36:44.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.573][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:36:44.575][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:36:44.576][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.577][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.582][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:36:44.584][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:36:44.585][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.585][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.591][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 19:36:44.592][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 19:36:44.593][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.594][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.600][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:36:44.601][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:36:44.601][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.602][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.608][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:36:44.609][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:44.610][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.611][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.617][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:36:44.618][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:36:44.619][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.620][ef$get] fields variable is a list.
biodb.INFO [2023-10-15 19:36:44.629][biodb::testThat]
biodb.INFO [2023-10-15 19:36:44.630][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-10-15 19:36:44.631][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 19:36:44.632][biodb::testThat]
biodb.DEBUG[2023-10-15 19:36:44.646][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2023-10-15 19:36:44.653][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2023-10-15 19:36:44.659][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2023-10-15 19:36:44.660][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-15 19:36:44.662][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2023-10-15 19:36:44.663][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-10-15 19:36:44.686][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-10-15 19:36:44.687][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-10-15 19:36:44.689][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 19:36:44.690][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:36:44.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:36:44.724][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:36:44.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:36:44.727][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:36:44.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-15 19:36:44.732][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:36:44.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:36:44.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:36:44.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:36:44.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.740][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 19:36:44.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 19:36:44.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.744][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 19:36:44.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 19:36:44.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.748][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-10-15 19:36:44.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-10-15 19:36:44.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.752][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-15 19:36:44.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-15 19:36:44.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.756][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:36:44.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:36:44.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.760][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:36:44.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:36:44.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.764][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:36:44.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:36:44.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.768][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:36:44.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:36:44.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.772][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-15 19:36:44.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:36:44.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.776][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-15 19:36:44.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:36:44.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.780][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 19:36:44.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 19:36:44.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.784][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 19:36:44.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 19:36:44.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.788][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:36:44.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:44.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.792][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:36:44.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:44.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.796][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-15 19:36:44.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:44.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.800][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-10-15 19:36:44.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:44.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.804][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:36:44.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:44.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.808][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:36:44.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:44.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.812][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-15 19:36:44.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:44.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.816][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:36:44.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:44.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.820][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:36:44.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:44.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.824][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:36:44.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:44.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.828][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:36:44.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:44.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.832][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:36:44.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:44.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.836][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:36:44.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:36:44.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.841][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:36:44.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:36:44.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:36:44.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:36:44.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.849][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:36:44.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:36:44.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:36:44.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:36:44.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:36:44.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:36:44.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:36:44.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:36:44.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:36:44.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:36:44.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:36:44.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:36:44.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:36:44.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:36:44.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-15 19:36:44.877][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2023-10-15 19:36:44.878][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-10-15 19:36:44.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-10-15 19:36:44.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.882][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-10-15 19:36:44.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-10-15 19:36:44.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.886][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-10-15 19:36:44.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-10-15 19:36:44.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-10-15 19:36:44.899][biodb::testThat]
biodb.INFO [2023-10-15 19:36:44.900][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2023-10-15 19:36:44.901][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 19:36:44.902][biodb::testThat]
biodb.TRACE[2023-10-15 19:36:44.906][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:36:44.907][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:44.908][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.909][ef$get] fields variable is a list.
biodb.DEBUG[2023-10-15 19:36:44.910][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2023-10-15 19:36:44.938][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:36:44.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:44.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.947][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:36:44.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:44.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:44.951][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:36:44.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:44.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:44.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-15 19:36:44.958][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-10-15 19:36:44.963][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[2023-10-15 19:36:44.987][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 19:36:44.989][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 19:36:44.992][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2023-10-15 19:36:45.800][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2023-10-15 19:36:46.532][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-15 19:36:46.534][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2023-10-15 19:36:46.548][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2023-10-15 19:36:46.551][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2023-10-15 19:36:46.566][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:36:46.567][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:36:46.568][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:46.569][ef$get] fields variable is a list.
biodb.INFO [2023-10-15 19:36:46.574][biodb::testThat]
biodb.INFO [2023-10-15 19:36:46.575][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2023-10-15 19:36:46.576][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 19:36:46.577][biodb::testThat]
biodb.TRACE[2023-10-15 19:36:46.616][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:36:46.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:46.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:46.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:46.620][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:36:46.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:46.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:46.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:46.624][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:36:46.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:46.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:46.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-15 19:36:46.732][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-10-15 19:36:46.736][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-15 19:36:46.751][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-10-15 19:36:46.752][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-15 19:36:46.754][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2023-10-15 19:36:46.779][biodb::testThat]
biodb.INFO [2023-10-15 19:36:46.781][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2023-10-15 19:36:46.782][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 19:36:46.783][biodb::testThat]
biodb.TRACE[2023-10-15 19:36:46.804][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-15 19:36:46.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-15 19:36:46.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:46.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:46.808][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-15 19:36:46.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-15 19:36:46.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:46.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:46.812][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-10-15 19:36:46.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-10-15 19:36:46.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:46.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:46.816][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-10-15 19:36:46.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-10-15 19:36:46.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:46.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:46.858][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-15 19:36:46.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-15 19:36:46.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:46.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:46.862][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-15 19:36:46.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-15 19:36:46.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:46.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:46.866][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-10-15 19:36:46.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-10-15 19:36:46.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:46.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:46.870][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-10-15 19:36:46.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-10-15 19:36:46.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:46.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-10-15 19:36:46.880][biodb::testThat]
biodb.INFO [2023-10-15 19:36:46.881][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-10-15 19:36:46.882][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 19:36:46.883][biodb::testThat]
biodb.INFO [2023-10-15 19:36:46.892][biodb::testThat]
biodb.INFO [2023-10-15 19:36:46.893][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-10-15 19:36:46.894][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 19:36:46.895][biodb::testThat]
biodb.INFO [2023-10-15 19:36:46.904][biodb::testThat]
biodb.INFO [2023-10-15 19:36:46.905][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2023-10-15 19:36:46.906][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 19:36:46.907][biodb::testThat]
biodb.DEBUG[2023-10-15 19:36:46.912][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2023-10-15 19:36:48.073][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2023-10-15 19:36:48.616][biodb::testThat]
biodb.INFO [2023-10-15 19:36:48.617][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2023-10-15 19:36:48.619][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 19:36:48.620][biodb::testThat]
biodb.TRACE[2023-10-15 19:36:48.642][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:36:48.644][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:48.645][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:48.647][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:48.648][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:36:48.650][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:36:48.651][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:48.653][ef$get] fields variable is a list.
biodb.INFO [2023-10-15 19:36:48.656][biodb::testThat]
biodb.INFO [2023-10-15 19:36:48.657][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2023-10-15 19:36:48.658][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 19:36:48.660][biodb::testThat]
biodb.TRACE[2023-10-15 19:36:48.679][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:36:48.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:48.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:48.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:48.683][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:36:48.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:48.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:48.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:48.687][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:36:48.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:36:48.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:48.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-15 19:36:48.772][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-10-15 19:36:48.775][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-15 19:36:48.777][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-10-15 19:36:48.778][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-15 19:36:48.779][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2023-10-15 19:36:48.848][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-10-15 19:36:48.851][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-15 19:36:48.852][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-10-15 19:36:48.853][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-15 19:36:48.855][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2023-10-15 19:36:48.871][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-10-15 19:36:48.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-10-15 19:36:48.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:48.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:48.881][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-15 19:36:48.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-15 19:36:48.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:48.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:48.890][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:36:48.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:36:48.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:48.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:48.894][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:36:48.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:36:48.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:48.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:48.898][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:36:48.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:36:48.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:48.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:48.902][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:36:48.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:36:48.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:48.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:36:48.906][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:36:48.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:36:48.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:36:48.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-15 19:36:48.919][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2023-10-15 19:36:48.934][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 19:36:48.936][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 19:36:48.951][private$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[2023-10-15 19:36:52.896][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[2023-10-15 19:37:04.242][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-15 19:37:04.245][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2023-10-15 19:37:04.257][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2023-10-15 19:37:05.496][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[2023-10-15 19:37:05.502][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 19:37:05.504][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 19:37:05.508][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2023-10-15 19:37:06.244][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2023-10-15 19:37:06.984][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-15 19:37:06.988][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2023-10-15 19:37:06.995][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2023-10-15 19:37:07.039][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2023-10-15 19:37:07.045][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 19:37:07.047][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 19:37:07.049][private$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[2023-10-15 19:37:07.797][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[2023-10-15 19:37:08.542][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-15 19:37:08.544][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2023-10-15 19:37:08.549][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2023-10-15 19:37:08.572][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-10-15 19:37:08.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-10-15 19:37:08.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:08.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-10-15 19:37:08.588][biodb::testThat]
biodb.INFO [2023-10-15 19:37:08.589][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2023-10-15 19:37:08.590][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 19:37:08.592][biodb::testThat]
biodb.TRACE[2023-10-15 19:37:08.596][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-10-15 19:37:08.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-10-15 19:37:08.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:08.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:08.603][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-15 19:37:08.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-15 19:37:08.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:08.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:08.610][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:37:08.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:37:08.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:08.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:08.617][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:37:08.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:37:08.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:08.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:08.623][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:37:08.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:37:08.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:08.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:08.628][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:37:08.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:37:08.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:08.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-15 19:37:08.668][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 19:37:08.670][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:37:08.671][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:37:08.682][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:37:08.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:37:08.685][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:37:08.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:37:08.693][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[2023-10-15 19:37:08.697][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 19:37:08.698][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 19:37:08.700][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2023-10-15 19:37:12.637][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2023-10-15 19:37:23.826][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-15 19:37:23.832][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2023-10-15 19:37:23.853][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2023-10-15 19:37:25.379][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2023-10-15 19:37:25.454][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-10-15 19:37:25.457][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2023-10-15 19:37:25.459][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2023-10-15 19:37:25.462][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-10-15 19:37:25.463][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-10-15 19:37:25.464][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-10-15 19:37:25.465][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-10-15 19:37:25.466][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-10-15 19:37:25.490][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 19:37:25.492][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:37:25.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:37:25.506][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:37:25.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:37:25.510][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:37:25.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:37:25.513][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2023-10-15 19:37:25.518][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 19:37:25.520][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 19:37:25.521][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2023-10-15 19:37:26.336][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2023-10-15 19:37:27.115][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-10-15 19:37:27.119][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2023-10-15 19:37:27.126][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2023-10-15 19:37:27.130][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 19:37:27.132][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:37:27.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:37:27.149][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:37:27.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:37:27.152][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:37:27.154][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[2023-10-15 19:37:27.155][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2023-10-15 19:37:27.158][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 19:37:27.160][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 19:37:27.163][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2023-10-15 19:37:27.930][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2023-10-15 19:37:28.707][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-10-15 19:37:28.711][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2023-10-15 19:37:28.718][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2023-10-15 19:37:28.723][private$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[2023-10-15 19:37:28.726][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-10-15 19:37:28.729][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-10-15 19:37:28.731][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-10-15 19:37:28.734][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 19:37:28.735][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:37:28.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:37:28.763][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:37:28.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:37:28.766][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:37:28.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-15 19:37:28.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:37:28.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:37:28.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:28.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:28.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:37:28.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:37:28.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:28.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:28.791][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 19:37:28.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 19:37:28.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:28.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:28.798][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 19:37:28.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 19:37:28.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:28.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:28.805][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-10-15 19:37:28.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-10-15 19:37:28.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:28.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:28.811][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-15 19:37:28.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-15 19:37:28.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:28.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:28.818][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:37:28.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:37:28.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:28.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:28.825][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:37:28.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:37:28.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:28.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:28.832][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:37:28.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:37:28.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:28.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:28.838][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:37:28.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:37:28.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:28.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:28.845][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-15 19:37:28.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:37:28.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:28.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:28.850][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-15 19:37:28.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:37:28.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:28.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:28.857][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 19:37:28.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 19:37:28.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:28.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:28.864][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 19:37:28.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 19:37:28.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:28.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:28.871][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:37:28.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:37:28.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:28.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:28.878][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:37:28.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:37:28.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:28.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:28.884][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-15 19:37:28.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:37:28.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:28.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:28.888][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-10-15 19:37:28.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:37:28.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:28.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:28.892][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:37:28.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:37:28.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:28.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:28.895][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:37:28.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:37:28.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:28.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:28.900][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-15 19:37:28.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:37:28.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:28.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:28.906][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:28.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:28.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:28.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:28.912][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:28.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:28.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:28.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:28.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:37:28.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:37:28.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:28.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:28.925][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:28.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:28.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:28.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:28.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:37:28.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:37:28.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:28.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:28.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:37:28.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:37:28.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:28.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:28.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:37:28.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:37:28.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:28.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-15 19:37:28.951][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 19:37:28.952][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:37:28.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:37:28.964][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:37:28.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:37:28.967][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:37:28.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-15 19:37:28.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:37:28.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:37:28.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:28.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:28.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:37:28.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:37:28.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:28.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:28.989][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 19:37:28.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 19:37:28.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:28.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.019][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-10-15 19:37:29.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-10-15 19:37:29.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.026][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-15 19:37:29.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-15 19:37:29.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.032][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:37:29.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:37:29.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.039][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:37:29.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:37:29.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.045][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:37:29.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:37:29.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.051][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:37:29.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:37:29.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.057][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-15 19:37:29.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:37:29.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.063][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-15 19:37:29.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:37:29.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.068][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 19:37:29.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 19:37:29.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.074][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 19:37:29.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 19:37:29.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.080][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:37:29.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:37:29.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.086][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:37:29.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:37:29.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.092][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-15 19:37:29.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:37:29.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.099][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-10-15 19:37:29.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:37:29.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.105][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:37:29.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:37:29.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.111][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:37:29.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:37:29.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.118][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-15 19:37:29.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:37:29.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.134][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.141][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:37:29.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:37:29.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.156][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:37:29.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:37:29.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:37:29.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:37:29.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:37:29.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:37:29.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:37:29.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:37:29.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:37:29.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:37:29.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:37:29.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:37:29.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:37:29.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:37:29.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:37:29.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:37:29.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:37:29.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:37:29.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-15 19:37:29.231][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2023-10-15 19:37:29.254][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-10-15 19:37:29.259][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 19:37:29.261][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:37:29.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:37:29.274][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:37:29.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:37:29.278][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:37:29.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-15 19:37:29.282][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.328][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.335][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:37:29.337][private$selectFields]
biodb.TRACE[2023-10-15 19:37:29.338][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-15 19:37:29.340][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-15 19:37:29.341][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:37:29.343][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.345][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.346][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.348][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.349][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.351][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.353][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.354][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.356][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:37:29.358][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:37:29.360][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.361][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.363][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.365][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.366][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-10-15 19:37:29.368][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.374][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.378][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.403][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-10-15 19:37:29.405][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 19:37:29.407][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:37:29.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:37:29.420][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:37:29.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:37:29.424][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:37:29.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-15 19:37:29.429][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.436][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.443][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:37:29.445][private$selectFields]
biodb.TRACE[2023-10-15 19:37:29.446][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-15 19:37:29.447][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-15 19:37:29.448][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:37:29.450][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.451][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.452][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.453][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.455][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.456][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.457][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.458][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.459][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:37:29.460][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:37:29.461][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.462][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.463][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.465][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.466][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-10-15 19:37:29.468][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.474][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.481][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.489][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-10-15 19:37:29.490][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 19:37:29.492][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:37:29.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:37:29.504][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:37:29.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:37:29.507][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:37:29.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-15 19:37:29.509][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.513][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.518][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:37:29.519][private$selectFields]
biodb.TRACE[2023-10-15 19:37:29.519][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-15 19:37:29.520][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-15 19:37:29.521][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:37:29.522][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.524][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.524][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.525][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.526][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.528][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.528][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.529][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.530][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:37:29.532][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:37:29.533][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.534][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.535][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.536][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.537][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-10-15 19:37:29.539][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.546][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.553][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:29.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.582][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-10-15 19:37:29.584][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-10-15 19:37:29.585][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-10-15 19:37:29.602][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-10-15 19:37:29.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-10-15 19:37:29.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-10-15 19:37:29.612][biodb::testThat]
biodb.INFO [2023-10-15 19:37:29.613][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2023-10-15 19:37:29.614][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 19:37:29.615][biodb::testThat]
biodb.TRACE[2023-10-15 19:37:29.618][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-10-15 19:37:29.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-10-15 19:37:29.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.626][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-15 19:37:29.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-15 19:37:29.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.633][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:37:29.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:37:29.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.639][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:37:29.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:37:29.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.644][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:37:29.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:37:29.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:29.648][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:37:29.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:37:29.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:29.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-15 19:37:29.733][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 19:37:29.735][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:37:29.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:37:29.748][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:37:29.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:37:29.751][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:37:29.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:37:29.759][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[2023-10-15 19:37:29.766][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 19:37:29.768][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 19:37:29.771][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.TRACE[2023-10-15 19:37:33.737][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375).
biodb.DEBUG[2023-10-15 19:37:44.511][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-15 19:37:44.514][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2023-10-15 19:37:44.524][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2023-10-15 19:37:45.436][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-10-15 19:37:45.458][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 19:37:45.459][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:37:45.460][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:37:45.466][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:37:45.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:37:45.468][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:37:45.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-15 19:37:45.481][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:45.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:45.485][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:45.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:45.509][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:37:45.510][private$selectFields]
biodb.TRACE[2023-10-15 19:37:45.511][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-15 19:37:45.512][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-15 19:37:45.513][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:37:45.514][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.515][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.516][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:45.517][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:45.518][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.519][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.520][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:45.521][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:45.522][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:37:45.560][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:37:45.562][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.563][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.564][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:45.565][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:45.566][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-10-15 19:37:45.567][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:45.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:45.572][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:45.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:45.576][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:45.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:45.580][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-10-15 19:37:45.582][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 19:37:45.583][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:37:45.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:37:45.591][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:37:45.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:37:45.593][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:37:45.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-15 19:37:45.595][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:45.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:45.599][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:45.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:45.604][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:37:45.604][private$selectFields]
biodb.TRACE[2023-10-15 19:37:45.605][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-15 19:37:45.606][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-15 19:37:45.607][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:37:45.608][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.610][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.611][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:45.612][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:45.613][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.614][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.615][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:45.616][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:45.617][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:37:45.618][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:37:45.619][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.620][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.621][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:45.622][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:45.623][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-10-15 19:37:45.624][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:45.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:45.628][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:45.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:45.632][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:45.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:45.637][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-10-15 19:37:45.638][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 19:37:45.639][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:37:45.640][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:37:45.646][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:37:45.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:37:45.648][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:37:45.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-15 19:37:45.651][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:45.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:45.655][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:45.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:45.659][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:37:45.660][private$selectFields]
biodb.TRACE[2023-10-15 19:37:45.661][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-15 19:37:45.662][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-15 19:37:45.663][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:37:45.664][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.665][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.666][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:45.667][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:45.668][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.669][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.670][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:45.671][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:45.672][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:37:45.673][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:37:45.674][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.676][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.677][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:45.678][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:45.679][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-10-15 19:37:45.680][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:45.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:45.684][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:45.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:45.688][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:45.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:45.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:45.693][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-10-15 19:37:45.694][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-10-15 19:37:45.695][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-10-15 19:37:45.706][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-10-15 19:37:45.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-10-15 19:37:45.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:45.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-10-15 19:37:45.715][biodb::testThat]
biodb.INFO [2023-10-15 19:37:45.716][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2023-10-15 19:37:45.717][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 19:37:45.718][biodb::testThat]
biodb.TRACE[2023-10-15 19:37:45.925][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-10-15 19:37:45.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-10-15 19:37:45.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:45.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:45.929][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-15 19:37:45.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-15 19:37:45.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:45.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:45.933][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:37:45.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:37:45.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:45.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:45.936][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:37:45.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:37:45.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:45.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:45.940][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:37:45.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:37:45.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:45.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:45.944][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:37:45.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:37:45.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:45.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-15 19:37:45.952][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 19:37:45.952][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:37:45.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:37:45.959][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:37:45.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:37:45.961][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:37:45.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:37:45.965][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2023-10-15 19:37:45.968][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-15 19:37:45.969][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2023-10-15 19:37:45.970][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-15 19:37:46.017][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2023-10-15 19:37:46.901][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-10-15 19:37:46.903][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 19:37:46.904][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:37:46.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:37:46.911][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:37:46.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:37:46.913][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:37:46.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-15 19:37:46.915][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:46.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:46.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:46.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:46.919][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:46.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:46.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:46.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:46.922][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:37:46.923][private$selectFields]
biodb.TRACE[2023-10-15 19:37:46.924][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-15 19:37:46.925][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-15 19:37:46.926][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:37:46.927][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:46.928][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:46.929][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:46.930][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:46.931][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:46.932][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:46.933][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:46.934][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:46.935][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:37:46.936][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:37:46.937][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:46.938][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:46.939][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:46.939][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:46.940][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-10-15 19:37:46.941][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:46.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:46.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:46.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:46.945][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:46.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:46.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:46.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:46.949][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:46.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:46.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:46.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:46.953][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-10-15 19:37:46.954][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 19:37:46.955][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:37:46.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:37:46.962][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:37:46.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:37:46.964][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:37:46.964][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.TRACE[2023-10-15 19:37:46.966][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:46.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:46.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:46.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:46.970][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:46.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:46.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:46.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:46.973][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:37:46.974][private$selectFields]
biodb.TRACE[2023-10-15 19:37:46.975][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-15 19:37:46.976][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-15 19:37:46.977][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:37:46.978][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:46.979][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:46.980][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:46.981][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:46.982][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:46.983][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:46.984][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:46.985][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:46.986][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:37:46.987][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:37:46.988][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:46.989][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:46.990][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:46.991][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:46.992][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-10-15 19:37:46.993][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:46.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:46.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:46.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:46.996][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:46.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:46.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:46.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:47.000][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:47.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:47.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:47.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:47.004][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-10-15 19:37:47.005][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 19:37:47.006][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:37:47.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:37:47.013][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:37:47.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:37:47.015][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:37:47.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-15 19:37:47.017][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:47.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:47.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:47.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:47.021][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:47.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:47.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:47.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:47.025][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:37:47.026][private$selectFields]
biodb.TRACE[2023-10-15 19:37:47.027][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-15 19:37:47.027][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-15 19:37:47.028][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:37:47.029][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:47.030][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:47.031][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:47.032][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:47.033][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:47.034][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:47.035][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:47.036][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:47.037][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:37:47.038][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:37:47.039][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:47.040][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:47.041][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:47.042][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:47.043][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-10-15 19:37:47.044][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:47.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:47.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:47.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:47.066][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:47.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:47.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:47.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:47.070][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:47.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:37:47.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:47.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:37:47.074][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-10-15 19:37:47.075][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-10-15 19:37:47.076][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-10-15 19:37:47.098][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-10-15 19:37:47.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-10-15 19:37:47.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:37:47.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-10-15 19:37:47.106][biodb::testThat]
biodb.INFO [2023-10-15 19:37:47.107][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2023-10-15 19:37:47.108][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 19:37:47.109][biodb::testThat]
biodb.DEBUG[2023-10-15 19:37:47.111][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2023-10-15 19:37:47.112][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2023-10-15 19:37:47.114][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2023-10-15 19:37:47.115][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-10-15 19:37:47.116][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-10-15 19:37:47.117][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-10-15 19:37:47.118][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-10-15 19:37:47.119][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-10-15 19:37:47.120][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-10-15 19:37:47.133][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 19:37:47.134][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:37:47.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:37:47.140][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:37:47.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:37:47.142][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:37:47.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:37:47.144][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2023-10-15 19:37:47.147][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 19:37:47.148][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 19:37:47.149][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-10-15 19:37:47.840][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-10-15 19:37:47.842][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 19:37:47.843][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-15 19:37:47.844][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-10-15 19:37:48.633][private$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[2023-10-15 19:37:48.635][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 19:37:48.636][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 19:37:48.638][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-10-15 19:37:49.335][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-10-15 19:37:49.336][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 19:37:49.337][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-15 19:37:49.338][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-10-15 19:37:50.173][private$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[2023-10-15 19:37:50.176][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 19:37:50.178][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 19:37:50.181][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-10-15 19:37:50.902][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-10-15 19:37:50.903][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 19:37:50.905][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-15 19:37:50.907][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-10-15 19:37:51.740][private$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[2023-10-15 19:37:51.742][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 19:37:51.745][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 19:37:51.748][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-10-15 19:37:52.469][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-10-15 19:37:52.470][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 19:37:52.472][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-15 19:37:52.474][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-10-15 19:37:53.319][private$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[2023-10-15 19:37:53.320][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 19:37:53.321][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 19:37:53.322][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-10-15 19:37:53.992][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-10-15 19:37:53.993][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 19:37:53.994][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-15 19:37:53.996][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-10-15 19:37:54.703][private$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[2023-10-15 19:37:54.705][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 19:37:54.707][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 19:37:54.709][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-10-15 19:37:55.442][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-10-15 19:37:55.444][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 19:37:55.445][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-15 19:37:55.447][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-10-15 19:37:56.238][private$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[2023-10-15 19:37:56.240][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 19:37:56.241][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 19:37:56.243][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-10-15 19:37:56.988][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-10-15 19:37:57.003][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 19:37:57.005][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-15 19:37:57.007][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-10-15 19:37:57.813][private$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[2023-10-15 19:37:57.815][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 19:37:57.817][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 19:37:57.820][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-10-15 19:37:58.527][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-10-15 19:37:58.529][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 19:37:58.531][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-15 19:37:58.533][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-10-15 19:37:59.353][private$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[2023-10-15 19:37:59.356][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 19:37:59.359][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 19:37:59.362][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-10-15 19:38:00.088][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-10-15 19:38:00.090][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 19:38:00.092][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-15 19:38:00.094][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-10-15 19:38:00.912][private$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[2023-10-15 19:38:00.914][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 19:38:00.915][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 19:38:00.916][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-10-15 19:38:01.605][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-10-15 19:38:01.608][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 19:38:01.610][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-10-15 19:38:01.612][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-10-15 19:38:02.417][private$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[2023-10-15 19:38:02.420][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2023-10-15 19:38:02.422][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-10-15 19:38:02.424][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-10-15 19:38:02.425][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-10-15 19:38:02.427][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 19:38:02.428][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:02.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:02.436][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:02.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:02.438][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:02.439][FUN] Functions in observer BiodbConfig: [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[2023-10-15 19:38:02.442][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:02.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:02.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:02.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:02.446][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:02.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:02.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:02.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:02.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:02.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:02.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:02.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:02.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:02.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:02.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:02.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:02.458][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:02.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:02.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:02.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:02.463][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:02.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:02.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:02.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:02.467][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:02.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:02.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:02.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:02.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:02.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:02.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:02.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-15 19:38:02.475][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2023-10-15 19:38:02.476][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2023-10-15 19:38:02.487][biodb::testThat]
biodb.INFO [2023-10-15 19:38:02.488][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2023-10-15 19:38:02.489][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 19:38:02.490][biodb::testThat]
biodb.DEBUG[2023-10-15 19:38:02.498][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2023-10-15 19:38:02.499][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2023-10-15 19:38:02.500][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-10-15 19:38:02.502][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2023-10-15 19:38:02.503][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2023-10-15 19:38:02.505][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-10-15 19:38:02.506][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-10-15 19:38:02.507][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-10-15 19:38:02.508][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-10-15 19:38:02.509][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-10-15 19:38:02.513][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 19:38:02.514][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:02.515][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:02.521][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:02.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:02.523][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:02.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:02.526][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2023-10-15 19:38:02.529][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 19:38:02.530][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 19:38:02.531][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-10-15 19:38:03.220][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-10-15 19:38:03.221][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 19:38:03.223][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[2023-10-15 19:38:03.224][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-10-15 19:38:03.930][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-10-15 19:38:03.932][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 19:38:03.933][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 19:38:03.935][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-10-15 19:38:04.618][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-10-15 19:38:04.620][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 19:38:04.622][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[2023-10-15 19:38:04.624][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-10-15 19:38:05.500][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-10-15 19:38:05.503][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 19:38:05.505][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 19:38:05.508][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-10-15 19:38:06.229][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-10-15 19:38:06.230][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 19:38:06.231][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[2023-10-15 19:38:06.232][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-10-15 19:38:07.029][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-10-15 19:38:07.031][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 19:38:07.032][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 19:38:07.033][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-10-15 19:38:07.711][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-10-15 19:38:07.712][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 19:38:07.714][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[2023-10-15 19:38:07.715][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-10-15 19:38:08.422][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-10-15 19:38:08.423][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 19:38:08.424][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 19:38:08.426][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-10-15 19:38:09.109][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-10-15 19:38:09.111][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 19:38:09.112][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[2023-10-15 19:38:09.114][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-10-15 19:38:09.855][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-10-15 19:38:09.856][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 19:38:09.858][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 19:38:09.860][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-10-15 19:38:10.583][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-10-15 19:38:10.585][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 19:38:10.586][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[2023-10-15 19:38:10.587][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-10-15 19:38:11.386][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-10-15 19:38:11.389][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 19:38:11.391][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 19:38:11.394][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-10-15 19:38:12.079][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-10-15 19:38:12.081][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 19:38:12.083][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[2023-10-15 19:38:12.084][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-10-15 19:38:12.910][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-10-15 19:38:12.912][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 19:38:12.913][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 19:38:12.914][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-10-15 19:38:13.617][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-10-15 19:38:13.620][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 19:38:13.622][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[2023-10-15 19:38:13.623][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-10-15 19:38:14.460][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-10-15 19:38:14.463][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 19:38:14.465][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 19:38:14.469][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-10-15 19:38:15.189][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-10-15 19:38:15.190][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 19:38:15.191][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[2023-10-15 19:38:15.192][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-10-15 19:38:16.029][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-10-15 19:38:16.031][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 19:38:16.032][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 19:38:16.034][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-10-15 19:38:16.727][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-10-15 19:38:16.729][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-10-15 19:38:16.730][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[2023-10-15 19:38:16.731][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-10-15 19:38:17.559][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-10-15 19:38:17.560][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 19:38:17.561][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:17.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:17.570][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:17.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:17.573][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:17.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:17.575][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2023-10-15 19:38:17.579][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 19:38:17.580][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 19:38:17.581][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2023-10-15 19:38:18.297][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.DEBUG[2023-10-15 19:38:19.020][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-10-15 19:38:19.024][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.content"
biodb.TRACE[2023-10-15 19:38:19.029][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.request"
biodb.TRACE[2023-10-15 19:38:19.033][private$doSaveContentToFile] Saving to cache [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv"
biodb.DEBUG[2023-10-15 19:38:19.036][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-10-15 19:38:19.038][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-10-15 19:38:19.040][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-10-15 19:38:19.043][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 19:38:19.044][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:19.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:19.056][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:19.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:19.059][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:19.061][FUN] Functions in observer BiodbConfig: [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[2023-10-15 19:38:19.064][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:19.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:19.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.071][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:19.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:19.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:19.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:19.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-15 19:38:19.085][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 19:38:19.086][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:19.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:19.098][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:19.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:19.102][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:19.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-15 19:38:19.112][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:19.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:19.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:19.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:19.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.166][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 19:38:19.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 19:38:19.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.170][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 19:38:19.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 19:38:19.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.174][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-10-15 19:38:19.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-10-15 19:38:19.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.179][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-10-15 19:38:19.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-10-15 19:38:19.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.183][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-15 19:38:19.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-15 19:38:19.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.187][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-15 19:38:19.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-15 19:38:19.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.192][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:38:19.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:38:19.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.196][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:38:19.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:38:19.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.200][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:38:19.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:38:19.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.205][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:38:19.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:38:19.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.209][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-15 19:38:19.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:38:19.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.213][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-15 19:38:19.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:38:19.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.217][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 19:38:19.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 19:38:19.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.221][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 19:38:19.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 19:38:19.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.230][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:38:19.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:19.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.235][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:38:19.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:19.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.239][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-15 19:38:19.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:19.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.244][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-10-15 19:38:19.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:19.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.248][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:38:19.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:19.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.253][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:38:19.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:19.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.258][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-15 19:38:19.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:19.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.263][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:38:19.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:19.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.267][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:38:19.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:19.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.271][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:38:19.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:19.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.276][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:38:19.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:19.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.280][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:38:19.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:19.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.285][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:19.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:19.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.289][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:19.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:19.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:19.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:19.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.298][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:19.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:19.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:19.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:19.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:19.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:19.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:19.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:19.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:19.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:19.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:19.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:19.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:19.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:19.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:19.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:19.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:19.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:19.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:19.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:19.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:19.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:19.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:19.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:19.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:19.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:19.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-15 19:38:19.378][self$createEntryFromContent] Accession numbers: NA, LMFA08040013.
biodb.DEBUG[2023-10-15 19:38:19.379][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2023-10-15 19:38:19.380][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2023-10-15 19:38:19.402][biodb::testThat]
biodb.INFO [2023-10-15 19:38:19.403][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2023-10-15 19:38:19.404][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 19:38:19.405][biodb::testThat]
biodb.INFO [2023-10-15 19:38:19.431][biodb::testThat]
biodb.INFO [2023-10-15 19:38:19.432][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2023-10-15 19:38:19.433][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 19:38:19.434][biodb::testThat]
biodb.INFO [2023-10-15 19:38:19.444][biodb::testThat]
biodb.INFO [2023-10-15 19:38:19.446][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2023-10-15 19:38:19.447][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 19:38:19.447][biodb::testThat]
biodb.DEBUG[2023-10-15 19:38:19.451][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[2023-10-15 19:38:19.454][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 19:38:19.455][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 19:38:19.457][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2023-10-15 19:38:23.508][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2023-10-15 19:38:35.115][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-15 19:38:35.119][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2023-10-15 19:38:35.130][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2023-10-15 19:38:36.026][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:38:36.027][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:36.028][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:36.029][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:36.030][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:38:36.031][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:38:36.032][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:36.033][ef$get] fields variable is a list.
biodb.INFO [2023-10-15 19:38:36.035][biodb::testThat]
biodb.INFO [2023-10-15 19:38:36.036][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2023-10-15 19:38:36.037][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 19:38:36.038][biodb::testThat]
biodb.ERROR[2023-10-15 19:38:36.054][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2023-10-15 19:38:36.073][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2023-10-15 19:38:36.089][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-10-15 19:38:36.090][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-10-15 19:38:36.092][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-10-15 19:38:36.093][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-10-15 19:38:36.094][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:36.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:36.096][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:36.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:36.098][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-10-15 19:38:36.110][biodb::testContext]
biodb.INFO [2023-10-15 19:38:36.111][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-15 19:38:36.112][biodb::testContext] Test context - Web services tests
biodb.INFO [2023-10-15 19:38:36.113][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-15 19:38:36.114][biodb::testContext]
biodb.INFO [2023-10-15 19:38:36.116][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.8.1.
biodb.DEBUG[2023-10-15 19:38:36.118][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-10-15 19:38:36.122][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-15 19:38:36.123][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-10-15 19:38:36.124][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-10-15 19:38:36.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.127][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[2023-10-15 19:38:36.128][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-10-15 19:38:36.129][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-10-15 19:38:36.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.132][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-10-15 19:38:36.134][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-10-15 19:38:36.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.138][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-10-15 19:38:36.139][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-10-15 19:38:36.140][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-10-15 19:38:36.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.143][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-10-15 19:38:36.144][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-10-15 19:38:36.146][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-10-15 19:38:36.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.149][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-10-15 19:38:36.150][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-10-15 19:38:36.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.154][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-10-15 19:38:36.155][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-10-15 19:38:36.156][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-10-15 19:38:36.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.160][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-10-15 19:38:36.161][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-10-15 19:38:36.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.165][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-10-15 19:38:36.166][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-10-15 19:38:36.167][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-10-15 19:38:36.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.171][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-10-15 19:38:36.172][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-10-15 19:38:36.173][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-10-15 19:38:36.186][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-10-15 19:38:36.187][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-10-15 19:38:36.188][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-10-15 19:38:36.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.191][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-10-15 19:38:36.192][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-10-15 19:38:36.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.196][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-10-15 19:38:36.197][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-10-15 19:38:36.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.200][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-10-15 19:38:36.201][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-10-15 19:38:36.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.204][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-10-15 19:38:36.205][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-10-15 19:38:36.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.209][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-10-15 19:38:36.210][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-10-15 19:38:36.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.213][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-10-15 19:38:36.214][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-10-15 19:38:36.218][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-10-15 19:38:36.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.222][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-10-15 19:38:36.223][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-10-15 19:38:36.224][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-10-15 19:38:36.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.227][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-10-15 19:38:36.229][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-15 19:38:36.230][self$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[2023-10-15 19:38:36.231][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:36.232][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-15 19:38:36.233][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:36.234][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-15 19:38:36.234][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-15 19:38:36.235][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-15 19:38:36.236][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-15 19:38:36.237][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-15 19:38:36.238][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:36.239][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-10-15 19:38:36.240][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-15 19:38:36.241][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:38:36.242][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:36.243][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-15 19:38:36.243][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-15 19:38:36.243][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-15 19:38:36.243][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-15 19:38:36.243][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-15 19:38:36.244][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-15 19:38:36.245][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 19:38:36.246][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 19:38:36.246][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-15 19:38:36.247][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 19:38:36.248][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 19:38:36.249][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-15 19:38:36.250][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:38:36.251][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-15 19:38:36.252][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-15 19:38:36.253][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-15 19:38:36.254][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:38:36.255][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-10-15 19:38:36.256][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-15 19:38:36.257][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-10-15 19:38:36.258][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:36.259][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-15 19:38:36.260][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:36.261][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-15 19:38:36.262][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-15 19:38:36.263][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-15 19:38:36.264][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-15 19:38:36.265][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-15 19:38:36.266][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:36.267][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-10-15 19:38:36.268][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-15 19:38:36.268][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:38:36.269][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:36.270][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-15 19:38:36.270][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-15 19:38:36.270][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-15 19:38:36.270][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-15 19:38:36.270][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-15 19:38:36.271][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-15 19:38:36.272][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 19:38:36.273][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 19:38:36.274][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-15 19:38:36.275][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 19:38:36.276][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 19:38:36.277][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-15 19:38:36.278][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:38:36.278][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-15 19:38:36.279][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-15 19:38:36.280][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-15 19:38:36.281][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:38:36.282][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-10-15 19:38:36.284][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:36.285][self$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[2023-10-15 19:38:36.286][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:36.287][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-15 19:38:36.288][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:36.289][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-15 19:38:36.290][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-15 19:38:36.291][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-15 19:38:36.291][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-15 19:38:36.292][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-15 19:38:36.293][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-15 19:38:36.294][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-10-15 19:38:36.295][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-15 19:38:36.296][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:38:36.297][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:36.298][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:38:36.299][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-15 19:38:36.300][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 19:38:36.301][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 19:38:36.302][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-15 19:38:36.303][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 19:38:36.304][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 19:38:36.304][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-15 19:38:36.305][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:38:36.306][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-15 19:38:36.307][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-15 19:38:36.308][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-15 19:38:36.309][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:38:36.310][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-10-15 19:38:36.312][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:36.313][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-10-15 19:38:36.314][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:36.315][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-15 19:38:36.316][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:36.317][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-15 19:38:36.318][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-15 19:38:36.319][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-15 19:38:36.320][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-15 19:38:36.321][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-15 19:38:36.322][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-15 19:38:36.322][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-10-15 19:38:36.323][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-15 19:38:36.324][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:38:36.335][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:36.336][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:38:36.337][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-15 19:38:36.338][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 19:38:36.339][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 19:38:36.340][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-15 19:38:36.341][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 19:38:36.342][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 19:38:36.342][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-15 19:38:36.343][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:38:36.344][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-15 19:38:36.345][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-15 19:38:36.346][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-15 19:38:36.347][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:38:36.348][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-15 19:38:36.349][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:36.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:36.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:36.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:36.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:36.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:36.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:36.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:36.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:36.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:36.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.371][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[2023-10-15 19:38:36.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:36.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:36.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:36.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:36.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:36.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:36.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:36.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:36.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.387][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[2023-10-15 19:38:36.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:36.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:36.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:36.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:36.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:36.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:36.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:36.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:36.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:36.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:36.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.409][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:36.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:36.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:36.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:36.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.416][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[2023-10-15 19:38:36.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:36.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:36.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.421][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-10-15 19:38:36.423][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-10-15 19:38:36.424][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-10-15 19:38:36.425][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-10-15 19:38:36.427][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-10-15 19:38:36.428][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-10-15 19:38:36.429][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-10-15 19:38:36.431][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-10-15 19:38:36.432][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-10-15 19:38:36.433][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-10-15 19:38:36.435][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-10-15 19:38:36.436][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-10-15 19:38:36.437][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-10-15 19:38:36.438][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-10-15 19:38:36.440][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-10-15 19:38:36.441][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-10-15 19:38:36.442][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-10-15 19:38:36.444][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-10-15 19:38:36.445][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-10-15 19:38:36.446][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-10-15 19:38:36.448][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-10-15 19:38:36.449][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-10-15 19:38:36.450][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-10-15 19:38:36.452][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-10-15 19:38:36.453][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-10-15 19:38:36.454][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-10-15 19:38:36.456][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-10-15 19:38:36.457][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-10-15 19:38:36.459][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-10-15 19:38:36.460][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-10-15 19:38:36.461][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-10-15 19:38:36.463][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-10-15 19:38:36.464][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-10-15 19:38:36.465][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-10-15 19:38:36.466][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-10-15 19:38:36.468][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-10-15 19:38:36.479][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-10-15 19:38:36.481][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-10-15 19:38:36.482][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-10-15 19:38:36.483][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-10-15 19:38:36.485][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-10-15 19:38:36.486][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-10-15 19:38:36.487][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-10-15 19:38:36.489][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-10-15 19:38:36.490][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-10-15 19:38:36.491][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-10-15 19:38:36.493][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-10-15 19:38:36.494][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-10-15 19:38:36.495][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-10-15 19:38:36.496][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-10-15 19:38:36.498][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-10-15 19:38:36.499][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-10-15 19:38:36.500][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-10-15 19:38:36.502][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-10-15 19:38:36.503][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-10-15 19:38:36.504][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-10-15 19:38:36.505][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-10-15 19:38:36.507][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-10-15 19:38:36.508][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-10-15 19:38:36.509][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-10-15 19:38:36.511][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-10-15 19:38:36.512][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-10-15 19:38:36.513][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-10-15 19:38:36.514][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-10-15 19:38:36.516][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-10-15 19:38:36.517][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-10-15 19:38:36.518][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-10-15 19:38:36.520][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-10-15 19:38:36.521][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-10-15 19:38:36.522][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-10-15 19:38:36.523][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-10-15 19:38:36.525][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-10-15 19:38:36.526][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-10-15 19:38:36.527][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-10-15 19:38:36.529][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-10-15 19:38:36.530][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-10-15 19:38:36.531][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-10-15 19:38:36.532][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-10-15 19:38:36.534][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-10-15 19:38:36.535][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-10-15 19:38:36.536][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-10-15 19:38:36.537][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-10-15 19:38:36.539][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-10-15 19:38:36.540][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-10-15 19:38:36.542][initialize] This is biodb version 1.8.1.
biodb.DEBUG[2023-10-15 19:38:36.543][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-15 19:38:36.543][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:36.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:36.545][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:36.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:36.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:36.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:36.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:36.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:36.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:36.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:36.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:36.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:36.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:36.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:36.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:36.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:36.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:36.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:36.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:36.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:36.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:36.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:36.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:36.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:36.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:36.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:36.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:36.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:36.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:36.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:36.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.587][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.DEBUG[2023-10-15 19:38:36.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:36.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:36.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:36.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:36.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.593][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[2023-10-15 19:38:36.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:36.596][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:36.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:36.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:36.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:36.602][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:36.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:36.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:36.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:36.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:36.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:36.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:36.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:36.624][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:36.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:36.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:36.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.628][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[2023-10-15 19:38:36.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:36.630][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:36.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:36.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:36.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:36.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:36.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:36.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:36.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:36.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:36.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:36.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:36.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:36.648][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:36.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:36.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:36.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:36.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:36.654][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:36.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:36.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:36.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:36.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:36.659][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-10-15 19:38:36.660][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-10-15 19:38:36.662][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-15 19:38:36.663][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-10-15 19:38:36.664][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:36.665][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-15 19:38:36.665][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:36.666][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-15 19:38:36.667][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:36.668][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-15 19:38:36.669][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-15 19:38:36.670][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-15 19:38:36.671][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:36.672][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-10-15 19:38:36.673][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-15 19:38:36.674][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-10-15 19:38:36.674][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-10-15 19:38:36.674][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-10-15 19:38:36.674][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-10-15 19:38:36.674][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-10-15 19:38:36.674][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-10-15 19:38:36.674][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-10-15 19:38:36.674][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-10-15 19:38:36.674][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-10-15 19:38:36.675][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-10-15 19:38:36.676][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-15 19:38:36.676][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-15 19:38:36.677][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-15 19:38:36.678][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 19:38:36.679][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 19:38:36.680][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-15 19:38:36.680][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 19:38:36.681][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 19:38:36.682][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-15 19:38:36.683][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-10-15 19:38:36.683][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-10-15 19:38:36.684][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-15 19:38:36.685][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-15 19:38:36.686][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:36.687][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:38:36.688][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-10-15 19:38:36.689][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-10-15 19:38:36.692][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-10-15 19:38:36.693][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-10-15 19:38:36.694][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-10-15 19:38:36.696][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-10-15 19:38:36.697][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-10-15 19:38:36.698][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-10-15 19:38:36.699][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-10-15 19:38:36.700][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-10-15 19:38:36.701][biodb::testThat]
biodb.INFO [2023-10-15 19:38:36.702][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2023-10-15 19:38:36.703][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 19:38:36.704][biodb::testThat]
biodb.DEBUG[2023-10-15 19:38:36.708][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.DEBUG[2023-10-15 19:38:36.712][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 19:38:36.713][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 19:38:36.714][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2023-10-15 19:38:37.446][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[2023-10-15 19:38:38.193][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-15 19:38:38.196][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2023-10-15 19:38:38.201][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2023-10-15 19:38:38.214][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[2023-10-15 19:38:38.218][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 19:38:38.219][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 19:38:38.222][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2023-10-15 19:38:38.955][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty).
biodb.DEBUG[2023-10-15 19:38:39.707][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-15 19:38:39.710][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2023-10-15 19:38:39.715][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2023-10-15 19:38:39.728][biodb::testThat]
biodb.INFO [2023-10-15 19:38:39.729][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2023-10-15 19:38:39.751][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 19:38:39.759][biodb::testThat]
biodb.INFO [2023-10-15 19:38:39.791][biodb::testThat]
biodb.INFO [2023-10-15 19:38:39.792][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2023-10-15 19:38:39.793][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 19:38:39.794][biodb::testThat]
biodb.DEBUG[2023-10-15 19:38:39.798][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2023-10-15 19:38:39.801][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 19:38:39.802][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 19:38:39.804][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2023-10-15 19:38:40.658][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2023-10-15 19:38:41.208][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-15 19:38:41.211][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2023-10-15 19:38:41.214][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2023-10-15 19:38:41.220][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[2023-10-15 19:38:41.223][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-15 19:38:41.224][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2023-10-15 19:38:41.225][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-15 19:38:41.227][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2023-10-15 19:38:41.233][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[2023-10-15 19:38:41.236][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 19:38:41.237][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 19:38:41.239][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2023-10-15 19:38:42.096][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2023-10-15 19:38:42.679][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-15 19:38:42.681][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2023-10-15 19:38:42.685][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2023-10-15 19:38:42.693][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2023-10-15 19:38:42.696][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 19:38:42.697][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 19:38:42.699][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2023-10-15 19:38:44.012][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2023-10-15 19:38:47.264][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-15 19:38:47.266][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2023-10-15 19:38:47.270][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2023-10-15 19:38:47.389][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[2023-10-15 19:38:47.392][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-15 19:38:47.393][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-15 19:38:47.395][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2023-10-15 19:38:48.728][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2023-10-15 19:38:52.225][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-15 19:38:52.227][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2023-10-15 19:38:52.232][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2023-10-15 19:38:52.354][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-10-15 19:38:52.355][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-10-15 19:38:52.357][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-10-15 19:38:52.357][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-10-15 19:38:52.358][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:52.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:52.360][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:52.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:52.385][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-10-15 19:38:52.390][biodb::testContext]
biodb.INFO [2023-10-15 19:38:52.391][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-15 19:38:52.392][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2023-10-15 19:38:52.393][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-15 19:38:52.394][biodb::testContext]
biodb.INFO [2023-10-15 19:38:52.396][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.8.1.
biodb.DEBUG[2023-10-15 19:38:52.397][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-10-15 19:38:52.401][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-15 19:38:52.402][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-10-15 19:38:52.403][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-10-15 19:38:52.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.407][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-10-15 19:38:52.408][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-10-15 19:38:52.409][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.411][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-10-15 19:38:52.412][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-10-15 19:38:52.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.416][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-10-15 19:38:52.417][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-10-15 19:38:52.418][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-10-15 19:38:52.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.421][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-10-15 19:38:52.422][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-10-15 19:38:52.423][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-10-15 19:38:52.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.427][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-10-15 19:38:52.428][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-10-15 19:38:52.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.431][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-10-15 19:38:52.432][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-10-15 19:38:52.433][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-10-15 19:38:52.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.436][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-10-15 19:38:52.437][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-10-15 19:38:52.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.441][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-10-15 19:38:52.442][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-10-15 19:38:52.443][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-10-15 19:38:52.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.446][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-10-15 19:38:52.447][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-10-15 19:38:52.448][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-10-15 19:38:52.449][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-10-15 19:38:52.450][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-10-15 19:38:52.451][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-10-15 19:38:52.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.454][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-10-15 19:38:52.455][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-10-15 19:38:52.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.459][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-10-15 19:38:52.460][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-10-15 19:38:52.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.463][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-10-15 19:38:52.464][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-10-15 19:38:52.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.467][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-10-15 19:38:52.468][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-10-15 19:38:52.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.472][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-10-15 19:38:52.473][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-10-15 19:38:52.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.476][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-10-15 19:38:52.477][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-10-15 19:38:52.481][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-10-15 19:38:52.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.485][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-10-15 19:38:52.485][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-10-15 19:38:52.487][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-10-15 19:38:52.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.490][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-10-15 19:38:52.492][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-15 19:38:52.493][self$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[2023-10-15 19:38:52.494][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:52.495][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-15 19:38:52.496][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:52.497][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-15 19:38:52.498][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-15 19:38:52.499][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-15 19:38:52.500][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-15 19:38:52.501][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-15 19:38:52.502][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:52.503][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-10-15 19:38:52.504][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-15 19:38:52.504][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:38:52.505][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:52.506][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-15 19:38:52.506][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-15 19:38:52.506][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-15 19:38:52.506][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-15 19:38:52.506][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-15 19:38:52.507][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-15 19:38:52.508][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 19:38:52.509][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 19:38:52.510][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-15 19:38:52.511][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 19:38:52.512][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 19:38:52.513][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-15 19:38:52.514][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:38:52.515][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-15 19:38:52.516][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-15 19:38:52.517][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-15 19:38:52.518][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:38:52.519][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-10-15 19:38:52.521][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-15 19:38:52.522][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-10-15 19:38:52.523][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:52.523][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-15 19:38:52.524][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:52.525][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-15 19:38:52.554][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-15 19:38:52.556][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-15 19:38:52.557][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-15 19:38:52.558][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-15 19:38:52.559][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:52.560][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-10-15 19:38:52.561][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-15 19:38:52.562][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:38:52.563][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:52.564][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-15 19:38:52.564][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-15 19:38:52.564][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-15 19:38:52.564][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-15 19:38:52.564][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-15 19:38:52.565][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-15 19:38:52.566][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 19:38:52.567][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 19:38:52.568][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-15 19:38:52.569][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 19:38:52.570][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 19:38:52.571][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-15 19:38:52.572][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:38:52.573][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-15 19:38:52.574][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-15 19:38:52.575][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-15 19:38:52.576][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:38:52.578][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-10-15 19:38:52.580][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:52.581][self$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[2023-10-15 19:38:52.582][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:52.583][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-15 19:38:52.584][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:52.585][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-15 19:38:52.586][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-15 19:38:52.587][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-15 19:38:52.588][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-15 19:38:52.589][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-15 19:38:52.590][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-15 19:38:52.591][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-10-15 19:38:52.592][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-15 19:38:52.593][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:38:52.595][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:52.596][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:38:52.597][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-15 19:38:52.598][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 19:38:52.599][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 19:38:52.600][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-15 19:38:52.601][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 19:38:52.602][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 19:38:52.603][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-15 19:38:52.604][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:38:52.605][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-15 19:38:52.606][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-15 19:38:52.607][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-15 19:38:52.608][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:38:52.609][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-10-15 19:38:52.611][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:52.612][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-10-15 19:38:52.613][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:52.614][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-15 19:38:52.615][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:52.616][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-15 19:38:52.617][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-15 19:38:52.618][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-15 19:38:52.619][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-15 19:38:52.620][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-15 19:38:52.621][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-15 19:38:52.622][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-10-15 19:38:52.623][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-15 19:38:52.624][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:38:52.625][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:52.626][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:38:52.628][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-15 19:38:52.629][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 19:38:52.630][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 19:38:52.631][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-15 19:38:52.632][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 19:38:52.633][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 19:38:52.634][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-15 19:38:52.635][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:38:52.636][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-15 19:38:52.637][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-15 19:38:52.638][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-15 19:38:52.639][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:38:52.640][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-15 19:38:52.641][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:52.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:52.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:52.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:52.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:52.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:52.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:52.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:52.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.661][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[2023-10-15 19:38:52.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:52.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:52.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:52.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:52.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:52.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:52.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:52.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:52.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:52.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:52.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:52.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:52.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:52.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:52.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:52.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:52.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:52.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:52.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.723][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[2023-10-15 19:38:52.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:52.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:52.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:52.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:52.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:52.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:52.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:52.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:52.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.742][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-10-15 19:38:52.743][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-10-15 19:38:52.745][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-10-15 19:38:52.746][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-10-15 19:38:52.748][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-10-15 19:38:52.749][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-10-15 19:38:52.750][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-10-15 19:38:52.752][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-10-15 19:38:52.753][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-10-15 19:38:52.754][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-10-15 19:38:52.756][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-10-15 19:38:52.757][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-10-15 19:38:52.758][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-10-15 19:38:52.760][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-10-15 19:38:52.761][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-10-15 19:38:52.762][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-10-15 19:38:52.764][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-10-15 19:38:52.765][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-10-15 19:38:52.766][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-10-15 19:38:52.768][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-10-15 19:38:52.769][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-10-15 19:38:52.770][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-10-15 19:38:52.772][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-10-15 19:38:52.773][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-10-15 19:38:52.775][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-10-15 19:38:52.776][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-10-15 19:38:52.777][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-10-15 19:38:52.779][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-10-15 19:38:52.780][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-10-15 19:38:52.782][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-10-15 19:38:52.783][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-10-15 19:38:52.784][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-10-15 19:38:52.786][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-10-15 19:38:52.787][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-10-15 19:38:52.788][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-10-15 19:38:52.790][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-10-15 19:38:52.791][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-10-15 19:38:52.793][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-10-15 19:38:52.794][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-10-15 19:38:52.795][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-10-15 19:38:52.797][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-10-15 19:38:52.798][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-10-15 19:38:52.800][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-10-15 19:38:52.801][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-10-15 19:38:52.802][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-10-15 19:38:52.804][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-10-15 19:38:52.805][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-10-15 19:38:52.807][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-10-15 19:38:52.808][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-10-15 19:38:52.809][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-10-15 19:38:52.811][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-10-15 19:38:52.812][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-10-15 19:38:52.813][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-10-15 19:38:52.815][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-10-15 19:38:52.816][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-10-15 19:38:52.817][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-10-15 19:38:52.819][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-10-15 19:38:52.820][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-10-15 19:38:52.822][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-10-15 19:38:52.823][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-10-15 19:38:52.824][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-10-15 19:38:52.826][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-10-15 19:38:52.827][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-10-15 19:38:52.828][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-10-15 19:38:52.830][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-10-15 19:38:52.831][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-10-15 19:38:52.832][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-10-15 19:38:52.834][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-10-15 19:38:52.835][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-10-15 19:38:52.837][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-10-15 19:38:52.838][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-10-15 19:38:52.839][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-10-15 19:38:52.841][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-10-15 19:38:52.842][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-10-15 19:38:52.843][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-10-15 19:38:52.845][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-10-15 19:38:52.846][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-10-15 19:38:52.848][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-10-15 19:38:52.849][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-10-15 19:38:52.850][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-10-15 19:38:52.852][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-10-15 19:38:52.853][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-10-15 19:38:52.854][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-10-15 19:38:52.856][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-10-15 19:38:52.858][initialize] This is biodb version 1.8.1.
biodb.DEBUG[2023-10-15 19:38:52.876][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-15 19:38:52.877][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:52.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:52.879][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:52.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:52.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:52.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:52.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:52.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:52.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:52.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:52.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:52.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:52.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:52.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:52.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:52.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:52.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:52.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:52.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:52.906][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:52.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:52.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:52.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.910][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[2023-10-15 19:38:52.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:52.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:52.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:52.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:52.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.916][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[2023-10-15 19:38:52.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:52.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:52.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:52.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:52.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:52.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:52.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:52.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:52.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:52.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:52.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:52.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:52.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.933][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[2023-10-15 19:38:52.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:52.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:52.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:52.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:52.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:52.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:52.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:52.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:52.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:52.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:52.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:52.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:52.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:52.954][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:52.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:52.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:52.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:52.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:52.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:52.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:52.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:52.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:52.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:52.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:52.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:52.971][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:52.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:52.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:52.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-15 19:38:52.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:52.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:52.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:52.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:52.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:52.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-15 19:38:52.983][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-10-15 19:38:52.984][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-10-15 19:38:52.986][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-15 19:38:52.987][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-10-15 19:38:52.988][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:52.989][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-15 19:38:52.990][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:52.991][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-15 19:38:52.992][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:52.993][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-15 19:38:52.994][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-15 19:38:52.995][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-15 19:38:52.996][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:52.997][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-10-15 19:38:52.998][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-15 19:38:52.999][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-10-15 19:38:52.999][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-10-15 19:38:52.999][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-10-15 19:38:52.999][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-10-15 19:38:52.999][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-10-15 19:38:52.999][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-10-15 19:38:52.999][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-10-15 19:38:52.999][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-10-15 19:38:52.999][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-10-15 19:38:53.000][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-10-15 19:38:53.001][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-15 19:38:53.001][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-15 19:38:53.002][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-15 19:38:53.003][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 19:38:53.004][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 19:38:53.005][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-15 19:38:53.006][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-15 19:38:53.007][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-15 19:38:53.008][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-15 19:38:53.009][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-10-15 19:38:53.009][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-10-15 19:38:53.020][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-15 19:38:53.022][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-15 19:38:53.023][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-10-15 19:38:53.024][self$setPropertyValue]
biodb.DEBUG[2023-10-15 19:38:53.025][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-10-15 19:38:53.026][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-10-15 19:38:53.030][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-10-15 19:38:53.031][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-10-15 19:38:53.032][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-10-15 19:38:53.033][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-10-15 19:38:53.034][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-10-15 19:38:53.035][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-10-15 19:38:53.037][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-10-15 19:38:53.037][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-10-15 19:38:53.039][biodb::testThat]
biodb.INFO [2023-10-15 19:38:53.040][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2023-10-15 19:38:53.041][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-15 19:38:53.042][biodb::testThat]
biodb.DEBUG[2023-10-15 19:38:53.046][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2023-10-15 19:38:53.049][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-15 19:38:53.051][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2023-10-15 19:38:53.052][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-15 19:38:53.105][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2023-10-15 19:38:54.193][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2023-10-15 19:38:54.194][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-10-15 19:38:54.196][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2023-10-15 19:38:54.197][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2023-10-15 19:38:54.199][loadFileContents] Loaded 2 files from cache: [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2023-10-15 19:38:54.200][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-10-15 19:38:54.201][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-10-15 19:38:54.203][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-10-15 19:38:54.204][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 19:38:54.205][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:54.206][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:54.212][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:54.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:54.214][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:54.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-15 19:38:54.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:54.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:54.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:54.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:54.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.227][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 19:38:54.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 19:38:54.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.231][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 19:38:54.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 19:38:54.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.235][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-10-15 19:38:54.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-10-15 19:38:54.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.239][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-15 19:38:54.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-15 19:38:54.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.243][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:38:54.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:38:54.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.247][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:38:54.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:38:54.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.251][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:38:54.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:38:54.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.255][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:38:54.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:38:54.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.259][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-15 19:38:54.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:38:54.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.263][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-15 19:38:54.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:38:54.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.267][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 19:38:54.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 19:38:54.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.271][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 19:38:54.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 19:38:54.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.275][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:38:54.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:54.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.279][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:38:54.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:54.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.283][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-15 19:38:54.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:54.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.287][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-10-15 19:38:54.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:54.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.291][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:38:54.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:54.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.295][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:38:54.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:54.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.299][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-15 19:38:54.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:54.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.303][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:38:54.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:54.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.307][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:38:54.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:54.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.311][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:38:54.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:54.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.315][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:38:54.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:54.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.319][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:38:54.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:54.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.323][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:54.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:54.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.327][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:54.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:54.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:54.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:54.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.335][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:54.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:54.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:54.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:54.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:54.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:54.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:54.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:54.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-15 19:38:54.382][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 19:38:54.383][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:54.384][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:54.390][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:54.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:54.391][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:54.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-15 19:38:54.396][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:54.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:54.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:54.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:54.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.404][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 19:38:54.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 19:38:54.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.408][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 19:38:54.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 19:38:54.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.412][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-10-15 19:38:54.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-10-15 19:38:54.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.416][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-15 19:38:54.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-15 19:38:54.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.420][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:38:54.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:38:54.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.424][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:38:54.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:38:54.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.428][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:38:54.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:38:54.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.432][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:38:54.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:38:54.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.435][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-15 19:38:54.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:38:54.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.439][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-10-15 19:38:54.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:38:54.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.443][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 19:38:54.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 19:38:54.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.447][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 19:38:54.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 19:38:54.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.451][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:38:54.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:54.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.455][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:38:54.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:54.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.459][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-15 19:38:54.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:54.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.463][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-10-15 19:38:54.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:54.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.466][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:38:54.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:54.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.470][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:38:54.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:54.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.474][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-10-15 19:38:54.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:54.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.478][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:54.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:54.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.482][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:54.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:54.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:54.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:54.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.489][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:54.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:54.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:54.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:54.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:54.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:54.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:54.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:54.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:54.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:54.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:54.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:54.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:54.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:54.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:54.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:54.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:54.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:54.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:54.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:54.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-15 19:38:54.539][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2023-10-15 19:38:54.542][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-10-15 19:38:54.543][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 19:38:54.544][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:54.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:54.551][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:54.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:54.552][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:54.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-15 19:38:54.555][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-15 19:38:54.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-15 19:38:54.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.559][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-15 19:38:54.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-15 19:38:54.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.563][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-10-15 19:38:54.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-10-15 19:38:54.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.566][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-10-15 19:38:54.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-10-15 19:38:54.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.570][private$selectFields] Fields none
biodb.TRACE[2023-10-15 19:38:54.571][private$selectFields]
biodb.TRACE[2023-10-15 19:38:54.572][private$selectFields] Fields is null: TRUE
biodb.TRACE[2023-10-15 19:38:54.573][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-15 19:38:54.574][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:38:54.575][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:54.576][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:54.577][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.577][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.578][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 19:38:54.579][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 19:38:54.580][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.581][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.582][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:38:54.583][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:38:54.584][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.585][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.586][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:38:54.587][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:38:54.588][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.588][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.589][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:38:54.590][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:38:54.591][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.592][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.593][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 19:38:54.594][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 19:38:54.595][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.596][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.597][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:38:54.598][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:54.599][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.600][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.601][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:54.602][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:54.602][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.603][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.604][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:54.605][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:54.606][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.607][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.608][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 19:38:54.609][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 19:38:54.610][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.611][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.612][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:38:54.613][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:38:54.614][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.614][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.615][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:38:54.616][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:38:54.617][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.618][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.619][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:38:54.620][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:38:54.621][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.622][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.623][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 19:38:54.624][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 19:38:54.625][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.626][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.627][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:38:54.628][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:54.628][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.629][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.630][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:54.631][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:54.632][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.633][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.634][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:38:54.635][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:38:54.636][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:54.637][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:54.638][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.639][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.640][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 19:38:54.641][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 19:38:54.642][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.643][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.644][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:38:54.645][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:38:54.646][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.646][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.647][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:38:54.648][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:38:54.649][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.650][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.651][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:38:54.652][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:38:54.653][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.654][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.655][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 19:38:54.666][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 19:38:54.667][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.668][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.669][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:38:54.670][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:54.671][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.672][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.673][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:54.674][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:54.674][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.675][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.676][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2023-10-15 19:38:54.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:54.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:54.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:54.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:54.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:54.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:54.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.689][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 19:38:54.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 19:38:54.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.693][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 19:38:54.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 19:38:54.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.696][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 19:38:54.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 19:38:54.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.700][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:38:54.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:38:54.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.704][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:38:54.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:38:54.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.708][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:38:54.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:38:54.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.712][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:38:54.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:38:54.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.715][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:38:54.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:38:54.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.719][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:38:54.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:38:54.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.723][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:38:54.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:38:54.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.727][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:38:54.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:38:54.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.731][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:38:54.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:38:54.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.734][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 19:38:54.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 19:38:54.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.738][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 19:38:54.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 19:38:54.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.742][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 19:38:54.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 19:38:54.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.746][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:38:54.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:54.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.750][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:38:54.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:54.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.754][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:38:54.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:54.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.757][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:54.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:54.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.761][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:54.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:54.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.765][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:54.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:54.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.775][private$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[2023-10-15 19:38:54.776][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-15 19:38:54.777][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:54.778][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:54.784][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:54.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:54.785][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:54.786][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.TRACE[2023-10-15 19:38:54.788][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-15 19:38:54.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-15 19:38:54.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.792][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-15 19:38:54.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-15 19:38:54.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.796][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-10-15 19:38:54.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-10-15 19:38:54.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.800][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-10-15 19:38:54.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-10-15 19:38:54.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.804][private$selectFields] Fields none
biodb.TRACE[2023-10-15 19:38:54.805][private$selectFields]
biodb.TRACE[2023-10-15 19:38:54.817][private$selectFields] Fields is null: TRUE
biodb.TRACE[2023-10-15 19:38:54.818][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-15 19:38:54.819][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:38:54.820][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:54.821][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:54.822][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.823][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.824][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 19:38:54.825][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 19:38:54.826][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.827][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.828][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:38:54.829][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:38:54.830][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.830][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.831][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:38:54.832][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:38:54.833][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.834][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.835][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:38:54.836][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:38:54.837][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.838][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.839][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 19:38:54.840][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 19:38:54.841][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.842][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.842][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:38:54.843][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:54.844][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.845][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.846][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:54.847][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:54.848][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.849][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.850][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:54.851][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:54.852][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.853][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.853][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 19:38:54.854][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 19:38:54.855][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.856][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.857][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:38:54.858][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:38:54.859][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.860][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.861][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:38:54.862][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:38:54.863][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.864][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.864][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:38:54.865][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:38:54.866][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.867][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.868][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 19:38:54.869][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 19:38:54.870][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.871][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.872][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:38:54.873][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:54.874][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.875][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.875][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:54.876][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:54.877][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.878][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.879][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:38:54.880][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-10-15 19:38:54.881][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:54.882][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:54.883][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.884][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.885][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 19:38:54.886][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 19:38:54.887][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.888][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.888][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:38:54.889][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:38:54.890][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.891][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.892][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:38:54.893][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:38:54.894][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.895][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.896][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:38:54.897][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:38:54.898][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.899][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.900][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 19:38:54.901][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 19:38:54.902][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.902][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.903][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:38:54.904][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:54.905][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.906][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.907][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:54.908][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:54.909][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.910][ef$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.911][private$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[2023-10-15 19:38:54.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:54.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:54.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:54.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:54.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-15 19:38:54.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-15 19:38:54.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.924][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 19:38:54.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 19:38:54.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.927][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 19:38:54.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 19:38:54.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.931][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-15 19:38:54.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-15 19:38:54.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.935][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:38:54.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:38:54.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.939][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:38:54.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:38:54.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.943][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:38:54.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-10-15 19:38:54.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.947][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:38:54.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:38:54.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.951][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:38:54.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:38:54.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.965][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:38:54.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-10-15 19:38:54.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.969][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:38:54.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:38:54.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.973][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:38:54.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:38:54.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.976][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:38:54.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-15 19:38:54.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.980][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 19:38:54.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 19:38:54.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.984][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 19:38:54.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 19:38:54.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.988][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-15 19:38:54.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-15 19:38:54.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.992][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:38:54.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:54.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.995][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:38:54.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:54.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:54.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:54.999][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-15 19:38:55.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-15 19:38:55.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:55.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:55.003][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:55.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:55.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:55.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:55.007][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:55.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:55.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:55.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:55.011][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:55.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-10-15 19:38:55.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-15 19:38:55.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-15 19:38:55.018][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000002, 137783, 42607281, N-(3S-hydroxydecanoyl)-L-serine, 275.173274, ...].
biodb.DEBUG[2023-10-15 19:38:55.019][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-10-15 19:38:55.020][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2023-10-15 19:38:55.032][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-10-15 19:38:55.035][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-10-15 19:38:55.036][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-10-15 19:38:55.037][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-10-15 19:38:55.038][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-15 19:38:55.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-15 19:38:55.040][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-15 19:38:55.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-15 19:38:55.042][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-10-15 19:38:55.043][FUN] Functions in observer 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 
 27.621   2.132 133.940

Example timings

biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings

nameusersystemelapsed
LipidmapsStructureConn0.9790.0973.382
LipidmapsStructureEntry0.1340.0020.136