Pierrick Roger
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/biodbLipidmaps |
| git_branch: master |
| git_last_commit: e8379ce |
| git_last_commit_date: 2022-03-17 09:41:39 -0400 (Thu, 17 Mar 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:02 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
To the developers/maintainers of the biodbLipidmaps package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 177/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbLipidmaps 1.1.1 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: biodbLipidmaps |
| Version: 1.1.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biodbLipidmaps.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings biodbLipidmaps_1.1.1.tar.gz |
| StartedAt: 2022-03-17 18:33:32 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:35:30 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 117.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbLipidmaps.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biodbLipidmaps.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings biodbLipidmaps_1.1.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/biodbLipidmaps.Rcheck' * using R Under development (unstable) (2021-11-21 r81221) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'biodbLipidmaps/DESCRIPTION' ... OK * this is package 'biodbLipidmaps' version '1.1.1' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'biodbLipidmaps' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking 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 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 ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
biodbLipidmaps.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL biodbLipidmaps
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'biodbLipidmaps' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'biodbLipidmaps'
finding HTML links ... done
LipidmapsStructureConn html
LipidmapsStructureEntry html
biodbLipidmaps-package html
** 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)
Making 'packages.html' ... done
biodbLipidmaps.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 [2022-03-17 18:34:17.002][biodb::testContext]
biodb.INFO [2022-03-17 18:34:17.002][biodb::testContext] ********************************************************************************
biodb.INFO [2022-03-17 18:34:17.002][biodb::testContext] Test context - Generic tests
biodb.INFO [2022-03-17 18:34:17.002][biodb::testContext] ********************************************************************************
biodb.INFO [2022-03-17 18:34:17.002][biodb::testContext]
biodb.INFO [2022-03-17 18:34:17.033][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.3.2.
biodb.DEBUG[2022-03-17 18:34:17.033][self$loadDefinitions] Load definitions from file "D:/biocbuild/bbs-3.15-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2022-03-17 18:34:17.049][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-03-17 18:34:17.049][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-03-17 18:34:17.049][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-03-17 18:34:17.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.049][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-03-17 18:34:17.064][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-03-17 18:34:17.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.064][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-03-17 18:34:17.064][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-03-17 18:34:17.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.080][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-03-17 18:34:17.080][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-03-17 18:34:17.080][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-03-17 18:34:17.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.080][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-03-17 18:34:17.096][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-03-17 18:34:17.096][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-03-17 18:34:17.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.096][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-03-17 18:34:17.096][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-03-17 18:34:17.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.096][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-03-17 18:34:17.096][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-03-17 18:34:17.096][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-03-17 18:34:17.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.111][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-03-17 18:34:17.111][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-03-17 18:34:17.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.111][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-03-17 18:34:17.111][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-03-17 18:34:17.111][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-03-17 18:34:17.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.111][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-03-17 18:34:17.111][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-03-17 18:34:17.111][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-03-17 18:34:17.111][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-03-17 18:34:17.111][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-03-17 18:34:17.111][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-03-17 18:34:17.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.127][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[2022-03-17 18:34:17.127][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-03-17 18:34:17.127][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-03-17 18:34:17.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.127][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-03-17 18:34:17.127][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-03-17 18:34:17.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.127][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[2022-03-17 18:34:17.127][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-03-17 18:34:17.127][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-03-17 18:34:17.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.127][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-03-17 18:34:17.127][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-03-17 18:34:17.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.142][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[2022-03-17 18:34:17.142][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-03-17 18:34:17.142][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-03-17 18:34:17.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.142][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-03-17 18:34:17.142][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-03-17 18:34:17.142][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2022-03-17 18:34:17.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.142][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[2022-03-17 18:34:17.142][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-03-17 18:34:17.142][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-03-17 18:34:17.142][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-03-17 18:34:17.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.158][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-03-17 18:34:17.174][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-03-17 18:34:17.189][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-03-17 18:34:17.189][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-03-17 18:34:17.189][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-03-17 18:34:17.189][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-03-17 18:34:17.189][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-03-17 18:34:17.189][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-03-17 18:34:17.189][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-03-17 18:34:17.189][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-03-17 18:34:17.189][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-03-17 18:34:17.189][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-03-17 18:34:17.205][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-03-17 18:34:17.205][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-03-17 18:34:17.205][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:34:17.205][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-03-17 18:34:17.205][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-03-17 18:34:17.205][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-03-17 18:34:17.205][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-03-17 18:34:17.205][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-03-17 18:34:17.205][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-03-17 18:34:17.205][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-03-17 18:34:17.205][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-03-17 18:34:17.205][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-03-17 18:34:17.205][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-03-17 18:34:17.205][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-03-17 18:34:17.205][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-03-17 18:34:17.205][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-03-17 18:34:17.205][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:34:17.205][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-03-17 18:34:17.205][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-03-17 18:34:17.205][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-03-17 18:34:17.205][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:34:17.205][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-03-17 18:34:17.221][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-03-17 18:34:17.221][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-03-17 18:34:17.221][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-03-17 18:34:17.221][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-03-17 18:34:17.221][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-03-17 18:34:17.221][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-03-17 18:34:17.221][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-03-17 18:34:17.221][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-03-17 18:34:17.221][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-03-17 18:34:17.221][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-03-17 18:34:17.221][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-03-17 18:34:17.221][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-03-17 18:34:17.221][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-03-17 18:34:17.221][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:34:17.221][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-03-17 18:34:17.221][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-03-17 18:34:17.221][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-03-17 18:34:17.221][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-03-17 18:34:17.221][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-03-17 18:34:17.221][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-03-17 18:34:17.221][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-03-17 18:34:17.236][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-03-17 18:34:17.236][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-03-17 18:34:17.236][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-03-17 18:34:17.236][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-03-17 18:34:17.236][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-03-17 18:34:17.236][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-03-17 18:34:17.236][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:34:17.236][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-03-17 18:34:17.236][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-03-17 18:34:17.236][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-03-17 18:34:17.236][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:34:17.236][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-03-17 18:34:17.236][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-03-17 18:34:17.236][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-03-17 18:34:17.236][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-03-17 18:34:17.236][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-03-17 18:34:17.236][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-03-17 18:34:17.236][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-03-17 18:34:17.252][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-03-17 18:34:17.252][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-03-17 18:34:17.252][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-03-17 18:34:17.252][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-03-17 18:34:17.252][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-03-17 18:34:17.252][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-03-17 18:34:17.252][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-03-17 18:34:17.252][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:34:17.252][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-03-17 18:34:17.252][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:34:17.252][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-03-17 18:34:17.252][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-03-17 18:34:17.252][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-03-17 18:34:17.267][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-03-17 18:34:17.267][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-03-17 18:34:17.267][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-03-17 18:34:17.267][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-03-17 18:34:17.267][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:34:17.267][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-03-17 18:34:17.267][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-03-17 18:34:17.267][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-03-17 18:34:17.267][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:34:17.267][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-03-17 18:34:17.267][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-03-17 18:34:17.267][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-03-17 18:34:17.267][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-03-17 18:34:17.267][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-03-17 18:34:17.267][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-03-17 18:34:17.267][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-03-17 18:34:17.267][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-03-17 18:34:17.267][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-03-17 18:34:17.283][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-03-17 18:34:17.283][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-03-17 18:34:17.283][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-03-17 18:34:17.283][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-03-17 18:34:17.283][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-03-17 18:34:17.283][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:34:17.283][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-03-17 18:34:17.283][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:34:17.283][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-03-17 18:34:17.283][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-03-17 18:34:17.283][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-03-17 18:34:17.283][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-03-17 18:34:17.283][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-03-17 18:34:17.283][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-03-17 18:34:17.283][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-03-17 18:34:17.283][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:34:17.283][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-03-17 18:34:17.283][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-03-17 18:34:17.299][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-03-17 18:34:17.299][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:34:17.299][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-03-17 18:34:17.299][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:17.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:17.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:17.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:17.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:17.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:17.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:17.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:17.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:17.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:17.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:17.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:17.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:17.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:17.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.330][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[2022-03-17 18:34:17.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:17.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:17.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.330][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[2022-03-17 18:34:17.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:17.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:17.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.330][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[2022-03-17 18:34:17.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:17.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:17.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.330][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[2022-03-17 18:34:17.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:17.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:17.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:17.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:17.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:17.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:17.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:17.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:17.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:17.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:17.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:17.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:17.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:17.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:17.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.361][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-03-17 18:34:17.361][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-03-17 18:34:17.377][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-03-17 18:34:17.377][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-03-17 18:34:17.377][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-03-17 18:34:17.377][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-03-17 18:34:17.377][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-03-17 18:34:17.377][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-03-17 18:34:17.377][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-03-17 18:34:17.377][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-03-17 18:34:17.377][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-03-17 18:34:17.377][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-03-17 18:34:17.377][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-03-17 18:34:17.377][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-03-17 18:34:17.377][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-03-17 18:34:17.377][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-03-17 18:34:17.392][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-03-17 18:34:17.392][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-03-17 18:34:17.392][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-03-17 18:34:17.392][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-03-17 18:34:17.392][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-03-17 18:34:17.392][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-03-17 18:34:17.392][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-03-17 18:34:17.392][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-03-17 18:34:17.392][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-03-17 18:34:17.392][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-03-17 18:34:17.392][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-03-17 18:34:17.392][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-03-17 18:34:17.392][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-03-17 18:34:17.408][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-03-17 18:34:17.408][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-03-17 18:34:17.408][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-03-17 18:34:17.408][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-03-17 18:34:17.408][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-03-17 18:34:17.408][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-03-17 18:34:17.408][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-03-17 18:34:17.408][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-03-17 18:34:17.408][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-03-17 18:34:17.424][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-03-17 18:34:17.424][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-03-17 18:34:17.424][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-03-17 18:34:17.424][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-03-17 18:34:17.424][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-03-17 18:34:17.424][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-03-17 18:34:17.424][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-03-17 18:34:17.424][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-03-17 18:34:17.424][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-03-17 18:34:17.439][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-03-17 18:34:17.439][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-03-17 18:34:17.439][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-03-17 18:34:17.439][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-03-17 18:34:17.439][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-03-17 18:34:17.439][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-03-17 18:34:17.439][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-03-17 18:34:17.439][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-03-17 18:34:17.439][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-03-17 18:34:17.439][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-03-17 18:34:17.439][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-03-17 18:34:17.439][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-03-17 18:34:17.439][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-03-17 18:34:17.455][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-03-17 18:34:17.455][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-03-17 18:34:17.455][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-03-17 18:34:17.455][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-03-17 18:34:17.455][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-03-17 18:34:17.455][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-03-17 18:34:17.455][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-03-17 18:34:17.455][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-03-17 18:34:17.455][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-03-17 18:34:17.455][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-03-17 18:34:17.455][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-03-17 18:34:17.455][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-03-17 18:34:17.455][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-03-17 18:34:17.471][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-03-17 18:34:17.471][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-03-17 18:34:17.471][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-03-17 18:34:17.471][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-03-17 18:34:17.471][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-03-17 18:34:17.471][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-03-17 18:34:17.471][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-03-17 18:34:17.471][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-03-17 18:34:17.471][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-03-17 18:34:17.471][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-03-17 18:34:17.486][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-03-17 18:34:17.486][initialize] This is biodb version 1.3.2.
biodb.DEBUG[2022-03-17 18:34:17.486][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-03-17 18:34:17.486][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:17.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:17.486][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:34:17.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:34:17.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:17.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:17.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:34:17.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:34:17.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:17.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:17.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:34:17.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:34:17.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:17.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:17.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:34:17.517][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:34:17.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:17.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:17.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:34:17.517][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:34:17.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:17.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:17.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:34:17.517][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:34:17.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:17.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:17.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:34:17.533][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:34:17.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:17.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:17.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:34:17.533][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:34:17.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:17.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:17.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:34:17.533][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:34:17.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:17.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:17.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:34:17.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:34:17.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:17.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:17.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:34:17.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:34:17.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:17.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:17.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:34:17.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:34:17.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:17.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:17.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.564][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[2022-03-17 18:34:17.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:34:17.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:34:17.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:17.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:17.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.564][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[2022-03-17 18:34:17.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:34:17.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:34:17.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:17.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:17.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.564][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[2022-03-17 18:34:17.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:34:17.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:34:17.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:17.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:17.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:34:17.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:34:17.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:17.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:17.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:34:17.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:34:17.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:34:17.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:17.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:17.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:17.580][biodb$loadDefinitions] Load definitions from file "D:/biocbuild/bbs-3.15-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2022-03-17 18:34:17.596][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2022-03-17 18:34:17.596][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-03-17 18:34:17.596][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-03-17 18:34:17.596][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-03-17 18:34:17.596][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-03-17 18:34:17.596][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-03-17 18:34:17.611][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-03-17 18:34:17.611][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-03-17 18:34:17.611][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-03-17 18:34:17.611][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-03-17 18:34:17.611][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-03-17 18:34:17.611][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-03-17 18:34:17.611][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2022-03-17 18:34:17.611][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-03-17 18:34:17.611][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2022-03-17 18:34:17.611][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2022-03-17 18:34:17.611][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2022-03-17 18:34:17.611][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2022-03-17 18:34:17.611][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2022-03-17 18:34:17.611][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2022-03-17 18:34:17.611][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2022-03-17 18:34:17.611][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2022-03-17 18:34:17.611][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2022-03-17 18:34:17.611][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-03-17 18:34:17.611][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-03-17 18:34:17.611][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-03-17 18:34:17.611][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-03-17 18:34:17.611][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-03-17 18:34:17.611][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-03-17 18:34:17.611][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-03-17 18:34:17.611][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-03-17 18:34:17.611][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-03-17 18:34:17.611][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-03-17 18:34:17.611][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-03-17 18:34:17.611][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2022-03-17 18:34:17.627][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-03-17 18:34:17.627][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-03-17 18:34:17.627][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-03-17 18:34:17.627][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:34:17.627][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2022-03-17 18:34:17.627][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-03-17 18:34:17.642][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2022-03-17 18:34:17.642][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2022-03-17 18:34:17.658][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2022-03-17 18:34:17.658][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2022-03-17 18:34:17.658][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-03-17 18:34:17.658][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-03-17 18:34:17.658][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2022-03-17 18:34:17.658][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2022-03-17 18:34:17.689][biodb::testThat]
biodb.INFO [2022-03-17 18:34:17.689][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2022-03-17 18:34:17.689][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-03-17 18:34:17.689][biodb::testThat]
biodb.TRACE[2022-03-17 18:34:17.705][loadFileContents] Loaded 1 files from cache: [1]: "D:/biocbuild/bbs-3.15-bioc/R/library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2022-03-17 18:34:17.705][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2022-03-17 18:34:17.705][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2022-03-17 18:34:17.721][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-03-17 18:34:17.721][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:34:17.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:34:17.736][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:17.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:17.736][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:17.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-03-17 18:34:17.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:17.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:17.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:17.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:17.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:17.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:17.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:17.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:17.767][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-03-17 18:34:17.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-03-17 18:34:17.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:17.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:17.767][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-03-17 18:34:17.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-03-17 18:34:17.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:17.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:17.783][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-03-17 18:34:17.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-03-17 18:34:17.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:17.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:17.783][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:34:17.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:34:17.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:17.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:17.814][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:34:17.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:34:17.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:17.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:17.814][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:34:17.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:34:17.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:17.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:17.830][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:34:17.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:34:17.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:17.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:17.830][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-03-17 18:34:17.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:17.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:17.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:17.846][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-03-17 18:34:17.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:17.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:17.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:17.846][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-03-17 18:34:17.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-03-17 18:34:17.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:17.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:17.846][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-03-17 18:34:17.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-03-17 18:34:17.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:17.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:17.861][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:17.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:17.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:17.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:17.877][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:17.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:17.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:17.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:17.877][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-03-17 18:34:17.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:17.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:17.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:17.892][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-03-17 18:34:17.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:17.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:17.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:17.892][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:17.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:17.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:17.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:17.892][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:17.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:17.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:17.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:17.892][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-03-17 18:34:17.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:17.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:17.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:17.924][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:17.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:17.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:17.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:17.924][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:17.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:17.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:17.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:17.955][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:17.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:17.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:17.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:17.955][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:17.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:17.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:17.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:17.955][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:17.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:17.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:17.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:17.971][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:17.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:17.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:17.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:17.971][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:17.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:17.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:17.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:17.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:17.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:17.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:17.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:17.986][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:17.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:17.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:17.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:17.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:17.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:17.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:17.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:17.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:17.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:17.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:17.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:17.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:18.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:18.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:18.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:18.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:18.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:18.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:18.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:18.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-03-17 18:34:18.017][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2022-03-17 18:34:18.033][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-03-17 18:34:18.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-03-17 18:34:18.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.033][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-03-17 18:34:18.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-03-17 18:34:18.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.033][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-03-17 18:34:18.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-03-17 18:34:18.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.033][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-03-17 18:34:18.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-03-17 18:34:18.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:18.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:18.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.096][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:18.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:18.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:18.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:18.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:18.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:18.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:18.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:18.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:18.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:18.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:18.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:18.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:18.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:18.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.127][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:18.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:18.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.127][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:18.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:18.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.127][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:18.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:18.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:18.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:18.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:18.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:18.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:18.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:18.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.158][ef$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:18.158][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:18.158][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.158][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:18.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:18.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.174][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:18.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:18.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.174][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:18.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:18.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.174][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:18.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:18.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.174][ef$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:18.174][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:18.174][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.174][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.174][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:18.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:18.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.189][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:34:18.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:34:18.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.189][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:34:18.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:34:18.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.189][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:34:18.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:34:18.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.205][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:34:18.205][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:34:18.205][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.205][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.205][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:34:18.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:34:18.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.221][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-03-17 18:34:18.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-03-17 18:34:18.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.221][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-03-17 18:34:18.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-03-17 18:34:18.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.221][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-03-17 18:34:18.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-03-17 18:34:18.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.236][ef$get] Asked field names are: formula.
biodb.TRACE[2022-03-17 18:34:18.236][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-03-17 18:34:18.236][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.236][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.236][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-03-17 18:34:18.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-03-17 18:34:18.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.236][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:18.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:18.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.252][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:18.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:18.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.252][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:18.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:18.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.252][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:18.252][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:18.252][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.252][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.252][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:18.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:18.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.267][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:34:18.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:34:18.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.267][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:34:18.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:34:18.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.267][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:34:18.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:34:18.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.267][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:34:18.283][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:34:18.283][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.283][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.283][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:34:18.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:34:18.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.283][ef$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:18.283][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:18.283][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.283][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.299][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:34:18.299][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:34:18.299][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.299][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.299][ef$get] Asked field names are: formula.
biodb.TRACE[2022-03-17 18:34:18.299][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-03-17 18:34:18.299][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.299][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.314][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:18.314][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:18.314][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.314][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.314][ef$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:18.314][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:18.314][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.314][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.330][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:34:18.330][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:34:18.330][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.330][ef$get] fields variable is a list.
biodb.INFO [2022-03-17 18:34:18.330][biodb::testThat]
biodb.INFO [2022-03-17 18:34:18.330][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2022-03-17 18:34:18.330][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-03-17 18:34:18.330][biodb::testThat]
biodb.DEBUG[2022-03-17 18:34:18.346][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2022-03-17 18:34:18.361][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2022-03-17 18:34:18.361][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2022-03-17 18:34:18.361][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-03-17 18:34:18.361][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2022-03-17 18:34:18.361][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2022-03-17 18:34:18.408][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2022-03-17 18:34:18.408][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2022-03-17 18:34:18.408][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-03-17 18:34:18.408][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:34:18.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:34:18.408][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:18.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:18.408][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:18.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-03-17 18:34:18.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:18.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:18.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:18.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:18.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.439][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-03-17 18:34:18.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-03-17 18:34:18.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.439][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-03-17 18:34:18.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-03-17 18:34:18.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.439][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-03-17 18:34:18.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-03-17 18:34:18.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.439][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:34:18.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:34:18.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.439][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:34:18.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:34:18.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.455][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:34:18.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:34:18.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.455][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:34:18.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:34:18.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.471][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-03-17 18:34:18.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:18.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.471][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-03-17 18:34:18.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:18.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.486][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-03-17 18:34:18.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-03-17 18:34:18.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.502][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-03-17 18:34:18.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-03-17 18:34:18.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.502][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:18.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:18.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.517][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:18.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:18.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.517][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-03-17 18:34:18.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:18.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.533][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-03-17 18:34:18.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:18.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.533][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:18.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:18.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.533][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:18.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:18.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.533][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-03-17 18:34:18.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:18.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.549][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:18.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:18.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.549][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:18.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:18.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.564][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:18.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:18.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.564][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:18.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:18.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.564][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:18.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:18.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.580][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:18.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:18.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.580][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:18.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:18.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:18.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:18.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.580][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:18.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:18.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:18.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:18.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:18.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:18.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:18.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:18.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:18.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:18.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:18.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:18.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:18.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:18.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-03-17 18:34:18.627][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2022-03-17 18:34:18.627][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2022-03-17 18:34:18.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2022-03-17 18:34:18.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.627][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2022-03-17 18:34:18.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2022-03-17 18:34:18.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.627][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2022-03-17 18:34:18.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2022-03-17 18:34:18.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-03-17 18:34:18.642][biodb::testThat]
biodb.INFO [2022-03-17 18:34:18.642][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2022-03-17 18:34:18.642][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-03-17 18:34:18.642][biodb::testThat]
biodb.TRACE[2022-03-17 18:34:18.642][ef$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:18.642][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:18.642][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.642][ef$get] fields variable is a list.
biodb.DEBUG[2022-03-17 18:34:18.642][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2022-03-17 18:34:18.674][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:18.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:18.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.674][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:18.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:18.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:18.674][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:18.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:18.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:18.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-03-17 18:34:18.689][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2022-03-17 18:34:18.752][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[2022-03-17 18:34:18.767][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-03-17 18:34:18.767][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-03-17 18:34:18.767][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2022-03-17 18:34:20.705][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride does not exist.
biodb.TRACE[2022-03-17 18:34:20.705][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-03-17 18:34:20.705][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-03-17 18:34:20.705][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2022-03-17 18:34:21.721][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-03-17 18:34:21.736][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2022-03-17 18:34:21.767][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2022-03-17 18:34:21.783][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2022-03-17 18:34:21.799][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:21.799][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:21.799][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:21.799][ef$get] fields variable is a list.
biodb.INFO [2022-03-17 18:34:21.799][biodb::testThat]
biodb.INFO [2022-03-17 18:34:21.799][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2022-03-17 18:34:21.799][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-03-17 18:34:21.799][biodb::testThat]
biodb.TRACE[2022-03-17 18:34:21.830][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:21.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:21.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:21.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:21.830][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:21.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:21.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:21.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:21.830][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:21.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:21.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:21.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-03-17 18:34:21.939][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2022-03-17 18:34:21.939][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-03-17 18:34:21.955][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2022-03-17 18:34:21.955][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-03-17 18:34:22.049][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2022-03-17 18:34:22.064][biodb::testThat]
biodb.INFO [2022-03-17 18:34:22.064][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2022-03-17 18:34:22.064][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-03-17 18:34:22.064][biodb::testThat]
biodb.TRACE[2022-03-17 18:34:22.111][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-03-17 18:34:22.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-03-17 18:34:22.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:22.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:22.127][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-03-17 18:34:22.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-03-17 18:34:22.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:22.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:22.127][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-03-17 18:34:22.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-03-17 18:34:22.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:22.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:22.127][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-03-17 18:34:22.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-03-17 18:34:22.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:22.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:22.205][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-03-17 18:34:22.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-03-17 18:34:22.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:22.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:22.205][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-03-17 18:34:22.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-03-17 18:34:22.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:22.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:22.221][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-03-17 18:34:22.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-03-17 18:34:22.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:22.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:22.221][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-03-17 18:34:22.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-03-17 18:34:22.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:22.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-03-17 18:34:22.236][biodb::testThat]
biodb.INFO [2022-03-17 18:34:22.236][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2022-03-17 18:34:22.236][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-03-17 18:34:22.236][biodb::testThat]
biodb.INFO [2022-03-17 18:34:22.236][biodb::testThat]
biodb.INFO [2022-03-17 18:34:22.236][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2022-03-17 18:34:22.236][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-03-17 18:34:22.236][biodb::testThat]
biodb.INFO [2022-03-17 18:34:22.252][biodb::testThat]
biodb.INFO [2022-03-17 18:34:22.252][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2022-03-17 18:34:22.252][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-03-17 18:34:22.252][biodb::testThat]
biodb.DEBUG[2022-03-17 18:34:22.252][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2022-03-17 18:34:22.533][getUrlContent] Use base::url() for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2022-03-17 18:34:24.221][biodb::testThat]
biodb.INFO [2022-03-17 18:34:24.221][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2022-03-17 18:34:24.236][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-03-17 18:34:24.236][biodb::testThat]
biodb.TRACE[2022-03-17 18:34:24.252][ef$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:24.252][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:24.252][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:24.252][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:24.252][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:24.252][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:24.252][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:24.252][ef$get] fields variable is a list.
biodb.INFO [2022-03-17 18:34:24.267][biodb::testThat]
biodb.INFO [2022-03-17 18:34:24.267][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2022-03-17 18:34:24.267][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-03-17 18:34:24.267][biodb::testThat]
biodb.TRACE[2022-03-17 18:34:24.283][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:24.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:24.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:24.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:24.299][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:24.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:24.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:24.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:24.299][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:24.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:24.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:24.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-03-17 18:34:24.439][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2022-03-17 18:34:24.439][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-03-17 18:34:24.439][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2022-03-17 18:34:24.439][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-03-17 18:34:24.439][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2022-03-17 18:34:24.486][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2022-03-17 18:34:24.486][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-03-17 18:34:24.486][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2022-03-17 18:34:24.486][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-03-17 18:34:24.502][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2022-03-17 18:34:24.502][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-03-17 18:34:24.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-03-17 18:34:24.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:24.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:24.517][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-03-17 18:34:24.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-03-17 18:34:24.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:24.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:24.549][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:24.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:24.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:24.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:24.549][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:24.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:24.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:24.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:24.549][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:24.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:24.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:24.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:24.549][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:24.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:24.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:24.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:24.549][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:24.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:24.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:24.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-03-17 18:34:24.611][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2022-03-17 18:34:24.627][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-03-17 18:34:24.627][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-03-17 18:34:24.642][private$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[2022-03-17 18:34:24.892][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06 does not exist.
biodb.TRACE[2022-03-17 18:34:24.908][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-03-17 18:34:24.908][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-03-17 18:34:24.908][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2022-03-17 18:34:32.674][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-03-17 18:34:32.674][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2022-03-17 18:34:32.783][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2022-03-17 18:34:35.236][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[2022-03-17 18:34:35.267][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-03-17 18:34:35.267][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-03-17 18:34:35.267][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2022-03-17 18:34:35.517][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06 does not exist.
biodb.TRACE[2022-03-17 18:34:35.517][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-03-17 18:34:35.517][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-03-17 18:34:35.517][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2022-03-17 18:34:36.392][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-03-17 18:34:36.392][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2022-03-17 18:34:36.408][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2022-03-17 18:34:36.517][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2022-03-17 18:34:36.517][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-03-17 18:34:36.517][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-03-17 18:34:36.517][private$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[2022-03-17 18:34:36.752][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06 does not exist.
biodb.TRACE[2022-03-17 18:34:36.752][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-03-17 18:34:36.908][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-03-17 18:34:36.908][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06).
biodb.DEBUG[2022-03-17 18:34:37.767][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-03-17 18:34:37.767][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2022-03-17 18:34:37.783][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2022-03-17 18:34:37.799][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-03-17 18:34:37.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-03-17 18:34:37.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:37.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-03-17 18:34:37.814][biodb::testThat]
biodb.INFO [2022-03-17 18:34:37.814][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2022-03-17 18:34:37.814][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-03-17 18:34:37.814][biodb::testThat]
biodb.TRACE[2022-03-17 18:34:37.814][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-03-17 18:34:37.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-03-17 18:34:37.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:37.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:37.830][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-03-17 18:34:37.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-03-17 18:34:37.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:37.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:37.830][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:37.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:37.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:37.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:37.830][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:37.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:37.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:37.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:37.830][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:37.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:37.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:37.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:37.830][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:37.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:37.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:37.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-03-17 18:34:37.861][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-03-17 18:34:37.861][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:34:37.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:34:37.861][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:37.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:37.861][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:37.861][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[2022-03-17 18:34:38.049][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[2022-03-17 18:34:38.049][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-03-17 18:34:38.049][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-03-17 18:34:38.049][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2022-03-17 18:34:38.314][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01 does not exist.
biodb.TRACE[2022-03-17 18:34:38.314][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-03-17 18:34:38.330][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-03-17 18:34:38.330][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2022-03-17 18:34:43.502][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-03-17 18:34:43.517][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2022-03-17 18:34:43.642][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2022-03-17 18:34:45.939][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2022-03-17 18:34:45.970][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2022-03-17 18:34:45.970][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2022-03-17 18:34:45.970][cch$loadFileContent] file.exist = [2]: "TRUE, FALSE".
biodb.TRACE[2022-03-17 18:34:45.970][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2022-03-17 18:34:45.970][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2022-03-17 18:34:45.986][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-03-17 18:34:45.986][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-03-17 18:34:45.986][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-03-17 18:34:45.986][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-03-17 18:34:45.986][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:34:45.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:34:45.986][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:45.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:45.986][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:45.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:45.986][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2022-03-17 18:34:46.002][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-03-17 18:34:46.002][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-03-17 18:34:46.002][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2022-03-17 18:34:46.267][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv does not exist.
biodb.TRACE[2022-03-17 18:34:46.283][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-03-17 18:34:46.283][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-03-17 18:34:46.283][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2022-03-17 18:34:47.158][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-03-17 18:34:47.174][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2022-03-17 18:34:47.205][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2022-03-17 18:34:47.220][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv"
biodb.DEBUG[2022-03-17 18:34:47.236][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-03-17 18:34:47.267][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2022-03-17 18:34:47.267][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2022-03-17 18:34:47.267][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-03-17 18:34:47.267][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:34:47.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:34:47.283][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:47.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:47.283][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:47.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-03-17 18:34:47.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:47.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:47.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:47.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:47.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.299][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-03-17 18:34:47.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-03-17 18:34:47.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.299][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-03-17 18:34:47.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-03-17 18:34:47.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.314][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-03-17 18:34:47.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-03-17 18:34:47.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.314][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-03-17 18:34:47.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-03-17 18:34:47.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.330][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:34:47.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:34:47.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.330][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:34:47.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:34:47.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.345][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:34:47.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:34:47.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.345][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:34:47.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:34:47.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.361][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-03-17 18:34:47.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:47.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.361][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-03-17 18:34:47.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:47.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.377][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-03-17 18:34:47.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-03-17 18:34:47.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.377][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-03-17 18:34:47.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-03-17 18:34:47.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.392][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:47.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:47.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.392][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:47.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:47.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.392][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-03-17 18:34:47.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:47.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.408][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-03-17 18:34:47.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:47.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.408][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:47.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:47.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.408][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:47.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:47.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.408][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-03-17 18:34:47.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:47.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.424][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.424][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:47.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:47.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.439][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:47.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:47.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:47.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:47.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:47.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:47.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-03-17 18:34:47.470][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-03-17 18:34:47.470][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:34:47.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:34:47.470][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:47.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:47.470][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:47.470][FUN] Functions in observer BiodbConfig: [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[2022-03-17 18:34:47.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:47.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:47.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:47.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:47.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.502][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-03-17 18:34:47.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-03-17 18:34:47.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.502][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-03-17 18:34:47.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-03-17 18:34:47.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.502][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-03-17 18:34:47.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-03-17 18:34:47.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.517][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:34:47.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:34:47.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.549][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:34:47.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:34:47.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.564][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:34:47.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:34:47.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.564][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:34:47.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:34:47.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.580][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-03-17 18:34:47.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:47.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.580][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-03-17 18:34:47.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:47.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.595][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-03-17 18:34:47.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-03-17 18:34:47.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.595][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-03-17 18:34:47.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-03-17 18:34:47.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.611][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:47.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:47.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.611][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:47.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:47.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.627][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-03-17 18:34:47.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:47.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.627][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-03-17 18:34:47.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:47.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.627][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:47.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:47.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.627][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:34:47.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:47.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.642][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-03-17 18:34:47.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:34:47.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.642][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.658][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:47.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:47.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.658][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:47.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:47.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:47.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:47.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:47.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:47.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:47.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:47.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:47.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:47.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:47.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:47.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:47.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:47.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:47.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:47.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:34:47.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:34:47.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-03-17 18:34:47.705][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2022-03-17 18:34:47.705][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2022-03-17 18:34:47.705][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-03-17 18:34:47.705][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:34:47.720][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:34:47.720][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:47.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:47.720][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:47.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-03-17 18:34:47.720][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.720][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.736][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:34:47.736][private$selectFields]
biodb.TRACE[2022-03-17 18:34:47.736][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-03-17 18:34:47.736][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-03-17 18:34:47.736][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:34:47.736][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.736][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.736][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.736][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.736][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.736][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.736][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.736][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.736][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:34:47.736][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:34:47.736][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.736][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.736][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.736][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.752][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-03-17 18:34:47.752][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.752][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.752][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.767][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2022-03-17 18:34:47.767][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-03-17 18:34:47.767][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:34:47.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:34:47.767][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:47.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:47.767][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:47.767][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[2022-03-17 18:34:47.767][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.783][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.783][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:34:47.783][private$selectFields]
biodb.TRACE[2022-03-17 18:34:47.783][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-03-17 18:34:47.783][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-03-17 18:34:47.783][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:34:47.783][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.783][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.783][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.783][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.783][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.783][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.799][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.799][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.799][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:34:47.799][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:34:47.799][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.799][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.799][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.799][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.814][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-03-17 18:34:47.814][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.814][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.814][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.814][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2022-03-17 18:34:47.814][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-03-17 18:34:47.830][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:34:47.830][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:34:47.830][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:47.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:47.830][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:47.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-03-17 18:34:47.830][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.830][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.845][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:34:47.845][private$selectFields]
biodb.TRACE[2022-03-17 18:34:47.845][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-03-17 18:34:47.845][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-03-17 18:34:47.845][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:34:47.845][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.845][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.845][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.845][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.845][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.845][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.845][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.845][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.845][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:34:47.845][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:34:47.845][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.845][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.845][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.845][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.861][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-03-17 18:34:47.861][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.861][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.861][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:47.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.861][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2022-03-17 18:34:47.861][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2022-03-17 18:34:47.861][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-03-17 18:34:47.877][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-03-17 18:34:47.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-03-17 18:34:47.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-03-17 18:34:47.877][biodb::testThat]
biodb.INFO [2022-03-17 18:34:47.877][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2022-03-17 18:34:47.877][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-03-17 18:34:47.877][biodb::testThat]
biodb.TRACE[2022-03-17 18:34:47.892][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-03-17 18:34:47.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-03-17 18:34:47.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.892][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-03-17 18:34:47.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-03-17 18:34:47.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.892][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:47.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:47.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.892][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:47.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:47.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.892][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:47.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:47.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:47.908][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:47.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:47.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:47.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-03-17 18:34:47.986][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-03-17 18:34:47.986][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:34:48.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:34:48.002][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:48.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:48.002][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:48.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:48.189][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.DEBUG[2022-03-17 18:34:48.205][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-03-17 18:34:48.205][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-03-17 18:34:48.205][private$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[2022-03-17 18:34:48.486][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375 does not exist.
biodb.TRACE[2022-03-17 18:34:48.486][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-03-17 18:34:48.486][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-03-17 18:34:48.486][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375).
biodb.DEBUG[2022-03-17 18:34:53.595][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-03-17 18:34:53.611][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2022-03-17 18:34:53.783][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2022-03-17 18:34:55.970][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2022-03-17 18:34:55.986][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-03-17 18:34:55.986][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:34:55.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:34:56.001][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:56.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:56.001][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:56.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-03-17 18:34:56.001][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:56.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:56.017][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:56.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:56.033][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:34:56.033][private$selectFields]
biodb.TRACE[2022-03-17 18:34:56.033][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-03-17 18:34:56.033][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-03-17 18:34:56.033][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:34:56.033][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.033][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.033][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:56.033][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:56.033][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.033][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.033][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:56.048][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:56.048][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:34:56.048][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:34:56.048][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.048][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.048][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:56.048][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:56.048][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-03-17 18:34:56.048][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:56.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:56.064][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:56.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:56.064][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:56.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:56.064][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2022-03-17 18:34:56.064][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-03-17 18:34:56.064][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:34:56.064][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:34:56.080][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:56.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:56.080][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:56.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-03-17 18:34:56.080][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:56.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:56.080][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:56.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:56.080][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:34:56.080][private$selectFields]
biodb.TRACE[2022-03-17 18:34:56.080][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-03-17 18:34:56.080][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-03-17 18:34:56.080][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:34:56.080][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.095][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.095][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:56.095][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:56.095][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.095][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.095][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:56.095][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:56.095][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:34:56.095][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:34:56.095][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.095][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.095][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:56.095][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:56.095][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-03-17 18:34:56.095][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:56.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:56.111][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:56.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:56.111][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:56.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:56.111][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2022-03-17 18:34:56.111][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-03-17 18:34:56.111][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:34:56.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:34:56.111][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:56.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:56.126][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:56.126][FUN] Functions in observer BiodbConfig: [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[2022-03-17 18:34:56.126][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:56.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:56.126][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:56.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:56.126][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:34:56.126][private$selectFields]
biodb.TRACE[2022-03-17 18:34:56.126][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-03-17 18:34:56.126][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-03-17 18:34:56.126][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:34:56.126][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.126][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.142][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:56.142][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:56.142][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.142][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.142][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:56.142][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:56.142][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:34:56.142][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:34:56.142][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.142][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.142][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:56.142][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:56.142][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-03-17 18:34:56.142][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:56.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:56.142][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:56.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:56.158][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:56.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:56.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:56.173][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2022-03-17 18:34:56.173][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2022-03-17 18:34:56.173][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-03-17 18:34:56.173][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-03-17 18:34:56.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-03-17 18:34:56.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:56.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-03-17 18:34:56.189][biodb::testThat]
biodb.INFO [2022-03-17 18:34:56.189][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2022-03-17 18:34:56.189][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-03-17 18:34:56.189][biodb::testThat]
biodb.TRACE[2022-03-17 18:34:56.189][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-03-17 18:34:56.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-03-17 18:34:56.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:56.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:56.189][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-03-17 18:34:56.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-03-17 18:34:56.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:56.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:56.189][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:56.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:56.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:56.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:56.189][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:56.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:56.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:56.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:56.205][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:56.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:56.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:56.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:56.205][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:56.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:34:56.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:56.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-03-17 18:34:56.220][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-03-17 18:34:56.220][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:34:56.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:34:56.236][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:56.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:56.236][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:56.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:56.392][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[2022-03-17 18:34:56.408][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-03-17 18:34:56.408][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2022-03-17 18:34:56.408][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-03-17 18:34:56.455][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2022-03-17 18:34:58.783][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2022-03-17 18:34:58.783][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-03-17 18:34:58.783][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:34:58.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:34:58.783][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:58.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:58.783][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:58.783][FUN] Functions in observer BiodbConfig: [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[2022-03-17 18:34:58.783][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:58.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:58.798][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:58.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:58.798][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:34:58.798][private$selectFields]
biodb.TRACE[2022-03-17 18:34:58.798][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-03-17 18:34:58.798][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-03-17 18:34:58.798][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:34:58.798][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.798][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.798][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:58.798][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:58.798][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.798][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.798][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:58.798][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:58.798][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:34:58.814][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:34:58.814][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.814][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.814][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:58.814][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:58.814][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-03-17 18:34:58.814][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:58.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:58.814][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:58.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:58.814][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:58.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:58.830][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2022-03-17 18:34:58.830][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-03-17 18:34:58.830][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:34:58.830][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:34:58.830][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:58.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:58.830][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:58.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-03-17 18:34:58.830][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:58.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:58.830][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:58.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:58.845][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:34:58.845][private$selectFields]
biodb.TRACE[2022-03-17 18:34:58.845][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-03-17 18:34:58.845][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-03-17 18:34:58.845][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:34:58.845][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.845][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.845][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:58.845][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:58.845][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.845][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.845][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:58.845][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:58.845][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:34:58.845][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:34:58.845][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.845][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.861][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:58.861][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:58.861][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-03-17 18:34:58.861][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:58.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:58.861][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:58.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:58.861][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:58.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:58.861][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2022-03-17 18:34:58.861][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-03-17 18:34:58.861][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:34:58.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:34:58.876][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:58.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:58.876][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:58.876][FUN] Functions in observer BiodbConfig: [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[2022-03-17 18:34:58.876][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:58.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:58.876][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:58.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:58.876][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:34:58.876][private$selectFields]
biodb.TRACE[2022-03-17 18:34:58.892][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-03-17 18:34:58.892][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-03-17 18:34:58.892][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:34:58.892][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.892][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.892][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:58.892][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:58.892][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.892][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.892][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:58.892][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:58.892][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:34:58.892][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:34:58.892][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.892][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.892][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:58.892][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:58.892][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-03-17 18:34:58.908][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:58.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:58.908][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:58.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:58.908][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:34:58.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:58.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:34:58.908][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2022-03-17 18:34:58.908][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2022-03-17 18:34:58.908][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-03-17 18:34:58.923][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-03-17 18:34:58.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-03-17 18:34:58.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:34:58.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-03-17 18:34:58.939][biodb::testThat]
biodb.INFO [2022-03-17 18:34:58.939][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2022-03-17 18:34:58.939][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-03-17 18:34:58.939][biodb::testThat]
biodb.DEBUG[2022-03-17 18:34:58.939][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2022-03-17 18:34:58.939][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2022-03-17 18:34:58.939][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2022-03-17 18:34:58.939][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-03-17 18:34:58.939][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-03-17 18:34:58.939][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2022-03-17 18:34:58.939][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-03-17 18:34:58.939][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-03-17 18:34:58.939][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-03-17 18:34:58.970][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-03-17 18:34:58.970][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:34:58.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:34:58.970][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:34:58.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:34:58.970][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:34:58.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:34:58.970][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2022-03-17 18:34:58.970][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-03-17 18:34:58.970][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-03-17 18:34:58.970][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-03-17 18:34:59.267][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-03-17 18:34:59.267][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-03-17 18:34:59.283][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[2022-03-17 18:34:59.283][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-03-17 18:35:00.158][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-03-17 18:35:00.158][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-03-17 18:35:00.158][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-03-17 18:35:00.158][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-03-17 18:35:00.439][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-03-17 18:35:00.439][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-03-17 18:35:00.439][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[2022-03-17 18:35:00.439][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-03-17 18:35:01.314][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-03-17 18:35:01.314][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-03-17 18:35:01.314][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-03-17 18:35:01.314][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-03-17 18:35:01.579][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-03-17 18:35:01.579][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-03-17 18:35:01.595][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[2022-03-17 18:35:01.595][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-03-17 18:35:02.486][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-03-17 18:35:02.486][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-03-17 18:35:02.486][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-03-17 18:35:02.486][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-03-17 18:35:02.783][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-03-17 18:35:02.783][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-03-17 18:35:02.783][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-03-17 18:35:02.783][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-03-17 18:35:03.673][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-03-17 18:35:03.673][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-03-17 18:35:03.673][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-03-17 18:35:03.673][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-03-17 18:35:03.954][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-03-17 18:35:03.954][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-03-17 18:35:03.954][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[2022-03-17 18:35:03.954][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-03-17 18:35:04.845][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-03-17 18:35:04.845][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-03-17 18:35:04.845][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-03-17 18:35:04.845][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-03-17 18:35:05.126][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-03-17 18:35:05.126][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-03-17 18:35:05.126][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[2022-03-17 18:35:05.126][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-03-17 18:35:06.048][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-03-17 18:35:06.048][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-03-17 18:35:06.048][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-03-17 18:35:06.064][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-03-17 18:35:06.361][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-03-17 18:35:06.361][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-03-17 18:35:06.361][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[2022-03-17 18:35:06.361][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-03-17 18:35:07.236][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-03-17 18:35:07.236][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-03-17 18:35:07.236][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-03-17 18:35:07.236][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-03-17 18:35:07.532][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-03-17 18:35:07.532][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-03-17 18:35:07.532][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[2022-03-17 18:35:07.532][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-03-17 18:35:08.423][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-03-17 18:35:08.423][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-03-17 18:35:08.423][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-03-17 18:35:08.423][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-03-17 18:35:08.689][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-03-17 18:35:08.704][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-03-17 18:35:08.704][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-03-17 18:35:08.704][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-03-17 18:35:09.595][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-03-17 18:35:09.595][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-03-17 18:35:09.595][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-03-17 18:35:09.595][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-03-17 18:35:09.876][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-03-17 18:35:09.876][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-03-17 18:35:09.876][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[2022-03-17 18:35:09.876][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-03-17 18:35:10.782][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.TRACE[2022-03-17 18:35:10.814][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2022-03-17 18:35:10.829][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-03-17 18:35:10.860][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2022-03-17 18:35:10.860][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2022-03-17 18:35:10.860][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-03-17 18:35:10.860][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:10.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:10.876][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:10.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:10.876][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:10.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-03-17 18:35:10.876][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:10.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:10.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:10.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:10.876][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:10.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:10.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:10.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:10.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:10.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:10.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:10.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:10.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:10.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:10.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:10.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:10.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:10.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:10.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:10.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:10.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:10.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:10.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:10.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:10.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:10.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:10.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:10.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:10.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:10.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:10.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:10.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-03-17 18:35:10.923][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2022-03-17 18:35:10.923][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2022-03-17 18:35:10.923][biodb::testThat]
biodb.INFO [2022-03-17 18:35:10.923][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2022-03-17 18:35:10.923][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-03-17 18:35:10.923][biodb::testThat]
biodb.DEBUG[2022-03-17 18:35:10.939][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2022-03-17 18:35:10.939][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2022-03-17 18:35:10.939][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2022-03-17 18:35:10.939][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2022-03-17 18:35:10.939][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2022-03-17 18:35:10.985][loadFileContents] Loaded 2 files from cache: [2]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv".
biodb.DEBUG[2022-03-17 18:35:10.985][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2022-03-17 18:35:11.032][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2022-03-17 18:35:11.032][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2022-03-17 18:35:11.032][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-03-17 18:35:11.032][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:11.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:11.032][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:11.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:11.048][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:11.048][FUN] Functions in observer BiodbConfig: [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[2022-03-17 18:35:11.048][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:11.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:11.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.048][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:11.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:11.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:11.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:11.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-03-17 18:35:11.064][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-03-17 18:35:11.064][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:11.064][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:11.064][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:11.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:11.079][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:11.079][FUN] Functions in observer BiodbConfig: [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[2022-03-17 18:35:11.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:11.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:11.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:11.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:11.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.095][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-03-17 18:35:11.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-03-17 18:35:11.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.110][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-03-17 18:35:11.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-03-17 18:35:11.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.126][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-03-17 18:35:11.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-03-17 18:35:11.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.142][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-03-17 18:35:11.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-03-17 18:35:11.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.142][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-03-17 18:35:11.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-03-17 18:35:11.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.157][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-03-17 18:35:11.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-03-17 18:35:11.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.157][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:35:11.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:35:11.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.173][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:35:11.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:35:11.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.173][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:35:11.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:35:11.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.189][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:35:11.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:35:11.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.189][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-03-17 18:35:11.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:35:11.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.204][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-03-17 18:35:11.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:35:11.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.204][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-03-17 18:35:11.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-03-17 18:35:11.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.220][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-03-17 18:35:11.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-03-17 18:35:11.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.220][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:35:11.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:11.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.235][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:35:11.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:11.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.235][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-03-17 18:35:11.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:11.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.251][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-03-17 18:35:11.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:11.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.251][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:35:11.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:11.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.251][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:35:11.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:11.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.251][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-03-17 18:35:11.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:11.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.267][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:35:11.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:11.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.267][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:35:11.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:11.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.267][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:35:11.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:11.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.282][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:35:11.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:11.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.282][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:35:11.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:11.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.298][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:11.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:11.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.314][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:11.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:11.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:11.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:11.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.314][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:11.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:11.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:11.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:11.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:11.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:11.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:11.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:11.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:11.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:11.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:11.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:11.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:11.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:11.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:11.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:11.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:11.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:11.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:11.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:11.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:11.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:11.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:11.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:11.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:11.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:11.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-03-17 18:35:11.376][self$createEntryFromContent] Accession numbers: NA, LMFA08040013.
biodb.DEBUG[2022-03-17 18:35:11.376][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2022-03-17 18:35:11.376][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2022-03-17 18:35:11.376][biodb::testThat]
biodb.INFO [2022-03-17 18:35:11.376][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2022-03-17 18:35:11.376][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-03-17 18:35:11.376][biodb::testThat]
biodb.INFO [2022-03-17 18:35:11.392][biodb::testThat]
biodb.INFO [2022-03-17 18:35:11.392][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2022-03-17 18:35:11.407][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-03-17 18:35:11.407][biodb::testThat]
biodb.INFO [2022-03-17 18:35:11.407][biodb::testThat]
biodb.INFO [2022-03-17 18:35:11.407][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2022-03-17 18:35:11.407][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-03-17 18:35:11.407][biodb::testThat]
biodb.DEBUG[2022-03-17 18:35:11.454][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[2022-03-17 18:35:11.454][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-03-17 18:35:11.454][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2022-03-17 18:35:11.454][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-03-17 18:35:11.485][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.TRACE[2022-03-17 18:35:13.626][ef$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:35:13.626][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:13.626][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:13.642][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:13.642][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:35:13.642][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:35:13.642][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:13.642][ef$get] fields variable is a list.
biodb.INFO [2022-03-17 18:35:13.642][biodb::testThat]
biodb.INFO [2022-03-17 18:35:13.642][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2022-03-17 18:35:13.642][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-03-17 18:35:13.642][biodb::testThat]
biodb.ERROR[2022-03-17 18:35:13.657][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2022-03-17 18:35:13.657][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2022-03-17 18:35:13.673][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-03-17 18:35:13.673][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2022-03-17 18:35:13.673][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2022-03-17 18:35:13.673][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-03-17 18:35:13.673][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:13.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:13.673][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:13.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:13.673][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:13.673][FUN] Functions in observer BiodbConfig: [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 [2022-03-17 18:35:13.689][biodb::testContext]
biodb.INFO [2022-03-17 18:35:13.689][biodb::testContext] ********************************************************************************
biodb.INFO [2022-03-17 18:35:13.689][biodb::testContext] Test context - Web services tests
biodb.INFO [2022-03-17 18:35:13.689][biodb::testContext] ********************************************************************************
biodb.INFO [2022-03-17 18:35:13.689][biodb::testContext]
biodb.INFO [2022-03-17 18:35:13.704][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.3.2.
biodb.DEBUG[2022-03-17 18:35:13.704][self$loadDefinitions] Load definitions from file "D:/biocbuild/bbs-3.15-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2022-03-17 18:35:13.704][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-03-17 18:35:13.704][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-03-17 18:35:13.704][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-03-17 18:35:13.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:13.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:13.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:13.704][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-03-17 18:35:13.704][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-03-17 18:35:13.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:13.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:13.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:13.720][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-03-17 18:35:13.720][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-03-17 18:35:13.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:13.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:13.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:13.720][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-03-17 18:35:13.720][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-03-17 18:35:13.720][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-03-17 18:35:13.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:13.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:13.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:13.720][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-03-17 18:35:13.720][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-03-17 18:35:13.720][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-03-17 18:35:13.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:13.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:13.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:13.720][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-03-17 18:35:13.735][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-03-17 18:35:13.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:13.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:13.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:13.735][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-03-17 18:35:13.735][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-03-17 18:35:13.735][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-03-17 18:35:13.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:13.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:13.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:13.735][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-03-17 18:35:13.735][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-03-17 18:35:13.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:13.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:13.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:13.735][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-03-17 18:35:13.735][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-03-17 18:35:13.735][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-03-17 18:35:13.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:13.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:13.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:13.751][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-03-17 18:35:13.751][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-03-17 18:35:13.751][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-03-17 18:35:13.751][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-03-17 18:35:13.751][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-03-17 18:35:13.751][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-03-17 18:35:13.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:13.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:13.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:13.751][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-03-17 18:35:13.751][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-03-17 18:35:13.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:13.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:13.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:13.751][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-03-17 18:35:13.751][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-03-17 18:35:13.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:13.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:13.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:13.767][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-03-17 18:35:13.767][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-03-17 18:35:13.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:13.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:13.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:13.767][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-03-17 18:35:13.767][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-03-17 18:35:13.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:13.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:13.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:13.767][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-03-17 18:35:13.767][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-03-17 18:35:13.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:13.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:13.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:13.767][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-03-17 18:35:13.767][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-03-17 18:35:13.782][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2022-03-17 18:35:13.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:13.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:13.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:13.782][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-03-17 18:35:13.782][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-03-17 18:35:13.782][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-03-17 18:35:13.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:13.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:13.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:13.782][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-03-17 18:35:13.798][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-03-17 18:35:13.798][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-03-17 18:35:13.798][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:13.798][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-03-17 18:35:13.798][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:13.814][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-03-17 18:35:13.814][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-03-17 18:35:13.814][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-03-17 18:35:13.814][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-03-17 18:35:13.814][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-03-17 18:35:13.814][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:13.814][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-03-17 18:35:13.814][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-03-17 18:35:13.814][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:35:13.814][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:13.814][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-03-17 18:35:13.814][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-03-17 18:35:13.814][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-03-17 18:35:13.814][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-03-17 18:35:13.814][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-03-17 18:35:13.814][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-03-17 18:35:13.814][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-03-17 18:35:13.814][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-03-17 18:35:13.814][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-03-17 18:35:13.814][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-03-17 18:35:13.814][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-03-17 18:35:13.814][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-03-17 18:35:13.814][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:35:13.829][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-03-17 18:35:13.829][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-03-17 18:35:13.829][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-03-17 18:35:13.829][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:35:13.829][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-03-17 18:35:13.829][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-03-17 18:35:13.829][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-03-17 18:35:13.829][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:13.829][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-03-17 18:35:13.845][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:13.845][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-03-17 18:35:13.845][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-03-17 18:35:13.845][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-03-17 18:35:13.845][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-03-17 18:35:13.845][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-03-17 18:35:13.845][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:13.845][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-03-17 18:35:13.845][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-03-17 18:35:13.845][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:35:13.845][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:13.845][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-03-17 18:35:13.845][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-03-17 18:35:13.845][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-03-17 18:35:13.845][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-03-17 18:35:13.845][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-03-17 18:35:13.845][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-03-17 18:35:13.860][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-03-17 18:35:13.860][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-03-17 18:35:13.860][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-03-17 18:35:13.860][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-03-17 18:35:13.860][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-03-17 18:35:13.860][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-03-17 18:35:13.860][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:35:13.860][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-03-17 18:35:13.860][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-03-17 18:35:13.860][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-03-17 18:35:13.860][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:35:13.860][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-03-17 18:35:13.860][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:13.860][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-03-17 18:35:13.860][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:13.860][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-03-17 18:35:13.860][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:13.860][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-03-17 18:35:13.876][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-03-17 18:35:13.876][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-03-17 18:35:13.876][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-03-17 18:35:13.876][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-03-17 18:35:13.876][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-03-17 18:35:13.876][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-03-17 18:35:13.876][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-03-17 18:35:13.876][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:35:13.876][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:13.876][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:35:13.876][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-03-17 18:35:13.876][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-03-17 18:35:13.876][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-03-17 18:35:13.876][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-03-17 18:35:13.876][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-03-17 18:35:13.876][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-03-17 18:35:13.876][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-03-17 18:35:13.876][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:35:13.876][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-03-17 18:35:13.876][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-03-17 18:35:13.892][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-03-17 18:35:13.892][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:35:13.892][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-03-17 18:35:13.892][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:13.892][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-03-17 18:35:13.892][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:13.892][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-03-17 18:35:13.892][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:13.892][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-03-17 18:35:13.892][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-03-17 18:35:13.892][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-03-17 18:35:13.892][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-03-17 18:35:13.892][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-03-17 18:35:13.892][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-03-17 18:35:13.892][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-03-17 18:35:13.892][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-03-17 18:35:13.892][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:35:13.907][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:13.907][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:35:13.907][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-03-17 18:35:13.907][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-03-17 18:35:13.907][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-03-17 18:35:13.907][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-03-17 18:35:13.907][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-03-17 18:35:13.907][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-03-17 18:35:13.907][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-03-17 18:35:13.907][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:35:13.907][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-03-17 18:35:13.907][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-03-17 18:35:13.907][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-03-17 18:35:13.907][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:35:13.907][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-03-17 18:35:13.907][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:13.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:13.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:13.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:13.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:13.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:13.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:13.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:13.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:13.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:13.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:13.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:13.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:13.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:13.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:13.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:13.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:13.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:13.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:13.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:13.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:13.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:13.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:13.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:13.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:13.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:13.939][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[2022-03-17 18:35:13.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:13.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:13.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:13.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:13.939][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[2022-03-17 18:35:13.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:13.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:13.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:13.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:13.939][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[2022-03-17 18:35:13.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:13.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:13.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:13.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:13.939][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[2022-03-17 18:35:13.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:13.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:13.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:13.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:13.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:13.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:13.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:13.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:13.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:13.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:13.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:13.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:13.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:13.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:13.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:13.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:13.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:13.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:13.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:13.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:13.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:13.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:13.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:13.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:13.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:13.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:13.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:13.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:13.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:13.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:13.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:13.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:13.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:13.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:13.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:13.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:13.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:13.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:13.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:13.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:13.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:13.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:13.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:13.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:13.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:13.985][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-03-17 18:35:13.985][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-03-17 18:35:13.985][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-03-17 18:35:13.985][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-03-17 18:35:13.985][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-03-17 18:35:13.985][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-03-17 18:35:13.985][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-03-17 18:35:13.985][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-03-17 18:35:13.985][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-03-17 18:35:13.985][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-03-17 18:35:13.985][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-03-17 18:35:13.985][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-03-17 18:35:13.985][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-03-17 18:35:13.985][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-03-17 18:35:14.001][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-03-17 18:35:14.001][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-03-17 18:35:14.001][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-03-17 18:35:14.001][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-03-17 18:35:14.001][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-03-17 18:35:14.001][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-03-17 18:35:14.001][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-03-17 18:35:14.001][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-03-17 18:35:14.001][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-03-17 18:35:14.001][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-03-17 18:35:14.001][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-03-17 18:35:14.001][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-03-17 18:35:14.001][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-03-17 18:35:14.017][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-03-17 18:35:14.017][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-03-17 18:35:14.017][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-03-17 18:35:14.017][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-03-17 18:35:14.017][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-03-17 18:35:14.017][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-03-17 18:35:14.017][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-03-17 18:35:14.017][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-03-17 18:35:14.017][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-03-17 18:35:14.017][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-03-17 18:35:14.017][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-03-17 18:35:14.017][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-03-17 18:35:14.017][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-03-17 18:35:14.017][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-03-17 18:35:14.032][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-03-17 18:35:14.032][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-03-17 18:35:14.032][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-03-17 18:35:14.032][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-03-17 18:35:14.032][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-03-17 18:35:14.032][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-03-17 18:35:14.032][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-03-17 18:35:14.032][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-03-17 18:35:14.032][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-03-17 18:35:14.032][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-03-17 18:35:14.032][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-03-17 18:35:14.032][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-03-17 18:35:14.032][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-03-17 18:35:14.048][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-03-17 18:35:14.048][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-03-17 18:35:14.048][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-03-17 18:35:14.048][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-03-17 18:35:14.048][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-03-17 18:35:14.048][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-03-17 18:35:14.048][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-03-17 18:35:14.048][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-03-17 18:35:14.048][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-03-17 18:35:14.048][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-03-17 18:35:14.048][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-03-17 18:35:14.048][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-03-17 18:35:14.048][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-03-17 18:35:14.048][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-03-17 18:35:14.064][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-03-17 18:35:14.064][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-03-17 18:35:14.064][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-03-17 18:35:14.064][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-03-17 18:35:14.064][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-03-17 18:35:14.064][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-03-17 18:35:14.079][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-03-17 18:35:14.079][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-03-17 18:35:14.079][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-03-17 18:35:14.079][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-03-17 18:35:14.079][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-03-17 18:35:14.079][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-03-17 18:35:14.079][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-03-17 18:35:14.079][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-03-17 18:35:14.079][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-03-17 18:35:14.079][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-03-17 18:35:14.079][initialize] This is biodb version 1.3.2.
biodb.DEBUG[2022-03-17 18:35:14.079][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-03-17 18:35:14.095][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:14.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:14.095][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:14.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:14.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:14.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:14.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:14.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:14.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:14.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:14.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:14.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:14.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:14.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:14.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:14.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:14.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:14.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:14.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:14.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:14.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:14.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:14.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:14.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:14.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:14.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:14.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:14.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:14.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:14.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:14.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:14.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:14.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:14.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:14.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:14.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:14.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:14.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:14.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:14.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:14.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:14.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:14.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:14.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:14.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:14.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:14.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:14.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:14.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:14.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:14.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:14.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:14.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:14.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:14.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:14.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:14.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:14.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:14.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:14.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:14.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:14.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:14.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:14.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:14.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:14.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:14.142][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[2022-03-17 18:35:14.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:14.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:14.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:14.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:14.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:14.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:14.142][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[2022-03-17 18:35:14.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:14.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:14.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:14.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:14.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:14.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:14.142][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[2022-03-17 18:35:14.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:14.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:14.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:14.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:14.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:14.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:14.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:14.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:14.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:14.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:14.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:14.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:14.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:14.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:14.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:14.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:14.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:14.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:14.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:14.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:14.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:14.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:14.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:14.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:14.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:14.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:14.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:14.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:14.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:14.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:14.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:14.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:14.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:14.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:14.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:14.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:14.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:14.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:14.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:14.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:14.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:14.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:14.173][biodb$loadDefinitions] Load definitions from file "D:/biocbuild/bbs-3.15-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2022-03-17 18:35:14.189][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2022-03-17 18:35:14.189][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-03-17 18:35:14.189][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-03-17 18:35:14.189][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:14.189][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-03-17 18:35:14.189][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:14.189][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-03-17 18:35:14.189][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:14.189][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-03-17 18:35:14.189][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-03-17 18:35:14.189][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-03-17 18:35:14.189][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:14.189][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2022-03-17 18:35:14.189][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-03-17 18:35:14.189][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2022-03-17 18:35:14.189][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2022-03-17 18:35:14.189][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2022-03-17 18:35:14.189][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2022-03-17 18:35:14.189][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2022-03-17 18:35:14.189][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2022-03-17 18:35:14.189][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2022-03-17 18:35:14.189][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2022-03-17 18:35:14.189][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2022-03-17 18:35:14.189][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-03-17 18:35:14.189][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-03-17 18:35:14.189][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-03-17 18:35:14.189][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-03-17 18:35:14.204][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-03-17 18:35:14.204][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-03-17 18:35:14.204][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-03-17 18:35:14.204][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-03-17 18:35:14.204][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-03-17 18:35:14.204][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-03-17 18:35:14.204][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-03-17 18:35:14.204][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2022-03-17 18:35:14.204][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-03-17 18:35:14.204][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-03-17 18:35:14.204][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:14.204][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:35:14.204][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2022-03-17 18:35:14.204][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-03-17 18:35:14.204][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2022-03-17 18:35:14.204][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2022-03-17 18:35:14.204][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2022-03-17 18:35:14.220][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2022-03-17 18:35:14.220][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-03-17 18:35:14.220][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-03-17 18:35:14.220][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2022-03-17 18:35:14.220][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2022-03-17 18:35:14.220][biodb::testThat]
biodb.INFO [2022-03-17 18:35:14.220][biodb::testThat] Running test function test_wsLmsdRecord_searchByName (" wsLmsdRecord() can search by name. ").
biodb.INFO [2022-03-17 18:35:14.220][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-03-17 18:35:14.220][biodb::testThat]
biodb.DEBUG[2022-03-17 18:35:14.267][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[2022-03-17 18:35:14.267][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-03-17 18:35:14.267][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cfd52aa1c2e3525a5defd7b7e8bd8bb8".
biodb.TRACE[2022-03-17 18:35:14.267][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-03-17 18:35:14.282][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content".
biodb.DEBUG[2022-03-17 18:35:14.360][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[2022-03-17 18:35:14.360][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-03-17 18:35:14.376][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4ae22a112f570b93d2a956448ab71bd0".
biodb.TRACE[2022-03-17 18:35:14.376][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-03-17 18:35:14.376][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content".
biodb.INFO [2022-03-17 18:35:14.376][biodb::testThat]
biodb.INFO [2022-03-17 18:35:14.376][biodb::testThat] Running test function test_wsLmsdRecord (" Test web service wsLmsdRecord. ").
biodb.INFO [2022-03-17 18:35:14.392][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-03-17 18:35:14.392][biodb::testThat]
biodb.INFO [2022-03-17 18:35:14.392][biodb::testThat]
biodb.INFO [2022-03-17 18:35:14.407][biodb::testThat] Running test function test_wsLmsdSearch (" Test web service wsLmsdSearch. ").
biodb.INFO [2022-03-17 18:35:14.407][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-03-17 18:35:14.407][biodb::testThat]
biodb.DEBUG[2022-03-17 18:35:14.454][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[2022-03-17 18:35:14.454][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-03-17 18:35:14.454][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2022-03-17 18:35:14.454][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-03-17 18:35:14.470][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2022-03-17 18:35:14.517][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[2022-03-17 18:35:14.517][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-03-17 18:35:14.517][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2022-03-17 18:35:14.517][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-03-17 18:35:14.517][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2022-03-17 18:35:14.579][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[2022-03-17 18:35:14.579][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-03-17 18:35:14.579][cch$loadFileContent] Trying to load 1 files from cache: [1]: "9edcc233717c530cf0cbf5f73b9c3fc7".
biodb.TRACE[2022-03-17 18:35:14.579][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-03-17 18:35:14.579][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content".
biodb.DEBUG[2022-03-17 18:35:14.642][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[2022-03-17 18:35:14.642][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-03-17 18:35:14.642][cch$loadFileContent] Trying to load 1 files from cache: [1]: "be9130a77f849b73da505cd10830451e".
biodb.TRACE[2022-03-17 18:35:14.642][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-03-17 18:35:14.657][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content".
biodb.DEBUG[2022-03-17 18:35:14.985][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[2022-03-17 18:35:14.985][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-03-17 18:35:14.985][cch$loadFileContent] Trying to load 1 files from cache: [1]: "6821b039f49696a2484834eb67daa971".
biodb.TRACE[2022-03-17 18:35:14.985][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-03-17 18:35:15.001][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content".
biodb.INFO [2022-03-17 18:35:15.282][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-03-17 18:35:15.282][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2022-03-17 18:35:15.282][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2022-03-17 18:35:15.282][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-03-17 18:35:15.282][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:15.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:15.282][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:15.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:15.282][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2022-03-17 18:35:15.298][biodb::testContext]
biodb.INFO [2022-03-17 18:35:15.298][biodb::testContext] ********************************************************************************
biodb.INFO [2022-03-17 18:35:15.298][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2022-03-17 18:35:15.298][biodb::testContext] ********************************************************************************
biodb.INFO [2022-03-17 18:35:15.298][biodb::testContext]
biodb.INFO [2022-03-17 18:35:15.313][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.3.2.
biodb.DEBUG[2022-03-17 18:35:15.313][self$loadDefinitions] Load definitions from file "D:/biocbuild/bbs-3.15-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2022-03-17 18:35:15.313][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-03-17 18:35:15.313][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-03-17 18:35:15.313][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-03-17 18:35:15.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.313][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-03-17 18:35:15.313][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-03-17 18:35:15.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.329][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-03-17 18:35:15.329][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-03-17 18:35:15.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.329][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-03-17 18:35:15.329][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-03-17 18:35:15.329][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-03-17 18:35:15.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.329][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-03-17 18:35:15.329][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-03-17 18:35:15.329][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-03-17 18:35:15.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.329][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-03-17 18:35:15.329][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-03-17 18:35:15.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.345][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-03-17 18:35:15.345][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-03-17 18:35:15.345][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-03-17 18:35:15.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.345][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-03-17 18:35:15.345][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-03-17 18:35:15.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.345][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-03-17 18:35:15.345][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-03-17 18:35:15.345][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-03-17 18:35:15.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.360][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-03-17 18:35:15.360][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-03-17 18:35:15.360][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-03-17 18:35:15.360][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-03-17 18:35:15.360][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-03-17 18:35:15.360][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-03-17 18:35:15.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.360][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-03-17 18:35:15.360][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-03-17 18:35:15.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.360][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-03-17 18:35:15.360][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-03-17 18:35:15.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.376][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-03-17 18:35:15.376][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-03-17 18:35:15.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.376][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-03-17 18:35:15.376][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-03-17 18:35:15.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.392][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.DEBUG[2022-03-17 18:35:15.392][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-03-17 18:35:15.392][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-03-17 18:35:15.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.392][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-03-17 18:35:15.392][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-03-17 18:35:15.392][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2022-03-17 18:35:15.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.392][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.DEBUG[2022-03-17 18:35:15.392][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-03-17 18:35:15.407][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-03-17 18:35:15.407][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-03-17 18:35:15.407][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.407][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-03-17 18:35:15.407][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-03-17 18:35:15.407][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-03-17 18:35:15.407][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:15.407][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-03-17 18:35:15.407][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:15.407][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-03-17 18:35:15.407][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-03-17 18:35:15.407][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-03-17 18:35:15.407][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-03-17 18:35:15.407][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-03-17 18:35:15.407][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:15.407][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-03-17 18:35:15.423][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-03-17 18:35:15.423][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:35:15.423][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:15.423][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-03-17 18:35:15.423][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-03-17 18:35:15.423][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-03-17 18:35:15.423][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-03-17 18:35:15.423][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-03-17 18:35:15.423][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-03-17 18:35:15.423][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-03-17 18:35:15.423][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-03-17 18:35:15.423][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-03-17 18:35:15.423][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-03-17 18:35:15.423][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-03-17 18:35:15.423][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-03-17 18:35:15.423][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:35:15.423][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-03-17 18:35:15.423][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-03-17 18:35:15.423][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-03-17 18:35:15.423][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:35:15.423][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-03-17 18:35:15.423][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-03-17 18:35:15.438][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-03-17 18:35:15.438][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:15.438][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-03-17 18:35:15.438][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:15.438][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-03-17 18:35:15.438][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-03-17 18:35:15.438][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-03-17 18:35:15.438][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-03-17 18:35:15.438][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-03-17 18:35:15.438][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:15.438][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-03-17 18:35:15.438][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-03-17 18:35:15.438][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:35:15.438][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:15.438][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-03-17 18:35:15.438][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-03-17 18:35:15.438][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-03-17 18:35:15.438][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-03-17 18:35:15.438][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-03-17 18:35:15.438][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-03-17 18:35:15.438][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-03-17 18:35:15.438][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-03-17 18:35:15.438][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-03-17 18:35:15.454][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-03-17 18:35:15.454][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-03-17 18:35:15.454][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-03-17 18:35:15.454][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:35:15.454][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-03-17 18:35:15.454][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-03-17 18:35:15.454][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-03-17 18:35:15.454][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:35:15.454][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-03-17 18:35:15.454][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:15.454][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-03-17 18:35:15.454][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:15.454][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-03-17 18:35:15.454][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:15.454][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-03-17 18:35:15.454][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-03-17 18:35:15.454][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-03-17 18:35:15.454][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-03-17 18:35:15.470][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-03-17 18:35:15.470][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-03-17 18:35:15.470][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-03-17 18:35:15.470][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-03-17 18:35:15.470][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:35:15.470][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:15.470][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:35:15.470][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-03-17 18:35:15.470][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-03-17 18:35:15.470][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-03-17 18:35:15.470][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-03-17 18:35:15.470][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-03-17 18:35:15.470][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-03-17 18:35:15.470][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-03-17 18:35:15.470][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:35:15.470][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-03-17 18:35:15.470][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-03-17 18:35:15.470][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-03-17 18:35:15.470][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:35:15.485][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-03-17 18:35:15.485][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:15.485][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-03-17 18:35:15.485][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:15.485][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-03-17 18:35:15.485][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:15.485][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-03-17 18:35:15.485][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-03-17 18:35:15.485][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-03-17 18:35:15.485][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-03-17 18:35:15.485][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-03-17 18:35:15.485][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-03-17 18:35:15.485][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-03-17 18:35:15.485][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-03-17 18:35:15.485][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:35:15.485][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:15.485][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:35:15.485][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-03-17 18:35:15.501][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-03-17 18:35:15.501][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-03-17 18:35:15.501][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-03-17 18:35:15.501][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-03-17 18:35:15.501][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-03-17 18:35:15.501][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-03-17 18:35:15.501][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:35:15.501][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-03-17 18:35:15.501][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-03-17 18:35:15.501][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-03-17 18:35:15.501][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:35:15.501][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-03-17 18:35:15.501][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:15.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:15.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:15.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:15.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:15.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:15.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:15.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:15.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:15.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:15.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:15.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:15.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:15.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:15.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:15.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:15.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:15.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:15.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:15.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:15.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:15.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:15.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:15.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:15.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:15.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:15.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:15.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:15.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:15.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:15.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:15.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:15.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:15.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:15.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.563][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-03-17 18:35:15.563][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-03-17 18:35:15.579][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-03-17 18:35:15.579][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-03-17 18:35:15.579][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-03-17 18:35:15.579][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-03-17 18:35:15.579][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-03-17 18:35:15.579][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-03-17 18:35:15.579][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-03-17 18:35:15.579][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-03-17 18:35:15.579][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-03-17 18:35:15.579][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-03-17 18:35:15.579][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-03-17 18:35:15.579][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-03-17 18:35:15.579][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-03-17 18:35:15.595][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-03-17 18:35:15.595][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-03-17 18:35:15.595][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-03-17 18:35:15.595][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-03-17 18:35:15.595][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-03-17 18:35:15.595][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-03-17 18:35:15.595][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-03-17 18:35:15.595][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-03-17 18:35:15.595][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-03-17 18:35:15.595][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-03-17 18:35:15.595][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-03-17 18:35:15.595][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-03-17 18:35:15.595][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-03-17 18:35:15.610][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-03-17 18:35:15.610][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-03-17 18:35:15.610][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-03-17 18:35:15.610][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-03-17 18:35:15.610][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-03-17 18:35:15.610][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-03-17 18:35:15.626][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-03-17 18:35:15.626][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-03-17 18:35:15.626][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-03-17 18:35:15.626][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-03-17 18:35:15.626][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-03-17 18:35:15.626][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-03-17 18:35:15.626][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-03-17 18:35:15.626][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-03-17 18:35:15.626][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-03-17 18:35:15.626][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-03-17 18:35:15.626][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-03-17 18:35:15.626][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-03-17 18:35:15.626][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-03-17 18:35:15.642][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-03-17 18:35:15.642][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-03-17 18:35:15.642][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-03-17 18:35:15.642][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-03-17 18:35:15.642][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-03-17 18:35:15.642][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-03-17 18:35:15.642][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-03-17 18:35:15.642][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-03-17 18:35:15.642][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-03-17 18:35:15.642][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-03-17 18:35:15.642][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-03-17 18:35:15.642][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-03-17 18:35:15.642][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-03-17 18:35:15.642][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-03-17 18:35:15.657][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-03-17 18:35:15.657][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-03-17 18:35:15.657][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-03-17 18:35:15.657][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-03-17 18:35:15.657][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-03-17 18:35:15.657][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-03-17 18:35:15.657][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-03-17 18:35:15.657][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-03-17 18:35:15.657][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-03-17 18:35:15.657][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-03-17 18:35:15.657][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-03-17 18:35:15.657][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-03-17 18:35:15.657][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-03-17 18:35:15.657][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-03-17 18:35:15.673][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-03-17 18:35:15.673][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-03-17 18:35:15.673][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-03-17 18:35:15.673][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-03-17 18:35:15.673][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-03-17 18:35:15.673][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-03-17 18:35:15.673][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-03-17 18:35:15.673][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-03-17 18:35:15.673][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-03-17 18:35:15.673][initialize] This is biodb version 1.3.2.
biodb.DEBUG[2022-03-17 18:35:15.673][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-03-17 18:35:15.673][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:15.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:15.673][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:15.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:15.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:15.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:15.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:15.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:15.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:15.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:15.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:15.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:15.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:15.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:15.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:15.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:15.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:15.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:15.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:15.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:15.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:15.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:15.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:15.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:15.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:15.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:15.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:15.720][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:15.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:15.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:15.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:15.720][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:15.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:15.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:15.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:15.720][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:15.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:15.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:15.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:15.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:15.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:15.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:15.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:15.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:15.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:15.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:15.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:15.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:15.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:15.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:15.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:15.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:15.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:15.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:15.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:15.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:15.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:15.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:15.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:15.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:15.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:15.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:15.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:15.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:15.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:15.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:15.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-03-17 18:35:15.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:15.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:15.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:15.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:15.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:15.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:15.767][biodb$loadDefinitions] Load definitions from file "D:/biocbuild/bbs-3.15-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2022-03-17 18:35:15.767][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2022-03-17 18:35:15.782][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-03-17 18:35:15.782][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-03-17 18:35:15.782][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:15.782][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-03-17 18:35:15.782][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:15.782][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-03-17 18:35:15.782][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:15.782][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-03-17 18:35:15.782][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-03-17 18:35:15.782][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-03-17 18:35:15.782][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:15.782][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2022-03-17 18:35:15.782][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-03-17 18:35:15.782][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2022-03-17 18:35:15.782][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2022-03-17 18:35:15.782][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2022-03-17 18:35:15.782][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2022-03-17 18:35:15.782][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2022-03-17 18:35:15.782][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2022-03-17 18:35:15.782][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2022-03-17 18:35:15.782][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2022-03-17 18:35:15.782][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2022-03-17 18:35:15.782][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-03-17 18:35:15.782][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-03-17 18:35:15.782][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-03-17 18:35:15.782][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-03-17 18:35:15.798][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-03-17 18:35:15.798][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-03-17 18:35:15.798][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-03-17 18:35:15.798][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-03-17 18:35:15.798][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-03-17 18:35:15.798][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-03-17 18:35:15.798][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-03-17 18:35:15.798][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2022-03-17 18:35:15.798][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-03-17 18:35:15.798][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-03-17 18:35:15.798][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-03-17 18:35:15.798][self$setPropertyValue]
biodb.DEBUG[2022-03-17 18:35:15.798][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2022-03-17 18:35:15.798][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-03-17 18:35:15.798][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2022-03-17 18:35:15.798][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2022-03-17 18:35:15.798][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2022-03-17 18:35:15.813][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2022-03-17 18:35:15.813][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-03-17 18:35:15.813][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-03-17 18:35:15.813][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2022-03-17 18:35:15.813][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2022-03-17 18:35:15.813][biodb::testThat]
biodb.INFO [2022-03-17 18:35:15.813][biodb::testThat] Running test function test_noOtherConnNeeded (" No other connector is needed. ").
biodb.INFO [2022-03-17 18:35:15.813][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-03-17 18:35:15.813][biodb::testThat]
biodb.DEBUG[2022-03-17 18:35:15.907][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[2022-03-17 18:35:15.907][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-03-17 18:35:15.907][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2022-03-17 18:35:15.923][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-03-17 18:35:15.938][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2022-03-17 18:35:18.063][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2022-03-17 18:35:18.063][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2022-03-17 18:35:18.063][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.INFO [2022-03-17 18:35:18.063][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.TRACE[2022-03-17 18:35:18.063][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2022-03-17 18:35:18.063][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-03-17 18:35:18.063][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2022-03-17 18:35:18.063][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-03-17 18:35:18.063][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-03-17 18:35:18.063][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-03-17 18:35:18.063][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-03-17 18:35:18.063][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:18.079][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:18.079][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:18.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:18.079][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:18.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:18.079][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.DEBUG[2022-03-17 18:35:18.079][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-03-17 18:35:18.079][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-03-17 18:35:18.079][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2022-03-17 18:35:18.345][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2022-03-17 18:35:18.345][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-03-17 18:35:18.360][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-03-17 18:35:18.360][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.DEBUG[2022-03-17 18:35:19.251][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-03-17 18:35:19.266][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f441f4b59d8c1fbcb63f4f502d20d459.content"
biodb.TRACE[2022-03-17 18:35:19.298][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f441f4b59d8c1fbcb63f4f502d20d459.request"
biodb.DEBUG[2022-03-17 18:35:19.298][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-03-17 18:35:19.298][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:19.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:19.313][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:19.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:19.313][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:19.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-03-17 18:35:19.313][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2022-03-17 18:35:19.313][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-03-17 18:35:19.313][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-03-17 18:35:19.313][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2022-03-17 18:35:19.579][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2022-03-17 18:35:19.579][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-03-17 18:35:19.595][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-03-17 18:35:19.595][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2022-03-17 18:35:20.501][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-03-17 18:35:20.516][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2022-03-17 18:35:20.548][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.TRACE[2022-03-17 18:35:20.563][private$doSaveContentToFile] Saving to cache [2]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv"
biodb.DEBUG[2022-03-17 18:35:20.579][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-03-17 18:35:20.595][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2022-03-17 18:35:20.595][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2022-03-17 18:35:20.595][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-03-17 18:35:20.595][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:20.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:20.610][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:20.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:20.610][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:20.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-03-17 18:35:20.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:20.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:20.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:20.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:20.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.626][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-03-17 18:35:20.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-03-17 18:35:20.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.626][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-03-17 18:35:20.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-03-17 18:35:20.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.626][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-03-17 18:35:20.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-03-17 18:35:20.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.641][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:35:20.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:35:20.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.641][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:35:20.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:35:20.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.657][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:35:20.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:35:20.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.657][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:35:20.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:35:20.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.673][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-03-17 18:35:20.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:35:20.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.673][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-03-17 18:35:20.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:35:20.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.688][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-03-17 18:35:20.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-03-17 18:35:20.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.688][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-03-17 18:35:20.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-03-17 18:35:20.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.704][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:35:20.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:20.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.704][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:35:20.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:20.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.704][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-03-17 18:35:20.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:20.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.720][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-03-17 18:35:20.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:20.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.735][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:35:20.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:20.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.735][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:35:20.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:20.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.735][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-03-17 18:35:20.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:20.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.751][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:35:20.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:20.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.751][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:35:20.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:20.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.751][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:35:20.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:20.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.751][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:35:20.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:20.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.766][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:35:20.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:20.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.766][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:20.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:20.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.782][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:20.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:20.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:20.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:20.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.782][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:20.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:20.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:20.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:20.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:20.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:20.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:20.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:20.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-03-17 18:35:20.798][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-03-17 18:35:20.798][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:20.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:20.813][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:20.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:20.813][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:20.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-03-17 18:35:20.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:20.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:20.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:20.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:20.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.829][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-03-17 18:35:20.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-03-17 18:35:20.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.829][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-03-17 18:35:20.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-03-17 18:35:20.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.845][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-03-17 18:35:20.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-03-17 18:35:20.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.845][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-03-17 18:35:20.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-03-17 18:35:20.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.860][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:35:20.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:35:20.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.860][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:35:20.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:35:20.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.876][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:35:20.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:35:20.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.876][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:35:20.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:35:20.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.891][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-03-17 18:35:20.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:35:20.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.891][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-03-17 18:35:20.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:35:20.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.907][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-03-17 18:35:20.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-03-17 18:35:20.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.907][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-03-17 18:35:20.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-03-17 18:35:20.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.923][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:35:20.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:20.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.923][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:35:20.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:20.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.938][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-03-17 18:35:20.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:20.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.938][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-03-17 18:35:20.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:20.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.938][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:35:20.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:20.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.938][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:35:20.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:20.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.954][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-03-17 18:35:20.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:20.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.954][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:20.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:20.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.970][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:20.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:20.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:20.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:20.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.985][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:20.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:20.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:20.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:20.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:20.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:20.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:20.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:20.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:20.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:20.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:21.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:21.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:21.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:21.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:21.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:21.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:21.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:21.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:21.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:21.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:21.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:21.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-03-17 18:35:21.016][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2022-03-17 18:35:21.032][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2022-03-17 18:35:21.032][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-03-17 18:35:21.032][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:21.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:21.032][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:21.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:21.032][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:21.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-03-17 18:35:21.032][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-03-17 18:35:21.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-03-17 18:35:21.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.048][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-03-17 18:35:21.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-03-17 18:35:21.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.048][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-03-17 18:35:21.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-03-17 18:35:21.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.048][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-03-17 18:35:21.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-03-17 18:35:21.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.048][private$selectFields] Fields none
biodb.TRACE[2022-03-17 18:35:21.048][private$selectFields]
biodb.TRACE[2022-03-17 18:35:21.048][private$selectFields] Fields is null: TRUE
biodb.TRACE[2022-03-17 18:35:21.048][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-03-17 18:35:21.048][private$selectFields] Fields [7]: "accession, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:35:21.048][ef$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:21.063][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:21.063][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.063][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.063][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:35:21.063][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:35:21.063][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.063][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.063][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:35:21.063][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:35:21.063][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.063][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.063][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:35:21.063][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:35:21.063][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.063][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.063][ef$get] Asked field names are: formula.
biodb.TRACE[2022-03-17 18:35:21.063][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-03-17 18:35:21.063][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.063][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.079][ef$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:35:21.079][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:21.079][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.079][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.079][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:21.079][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:21.079][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.079][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.079][ef$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:21.079][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:21.079][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.079][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.079][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:35:21.079][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:35:21.079][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.079][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.079][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:35:21.079][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:35:21.095][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.095][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.095][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:35:21.095][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:35:21.095][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.095][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.095][ef$get] Asked field names are: formula.
biodb.TRACE[2022-03-17 18:35:21.095][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-03-17 18:35:21.095][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.095][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.095][ef$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:35:21.095][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:21.095][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.095][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.095][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:21.095][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:21.095][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.095][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.110][private$selectFields] Fields [7]: "accession, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:35:21.110][private$organizeFieldsByGroups] Fields [7]: "accession, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:35:21.110][ef$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:21.110][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:21.110][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.110][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.110][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:35:21.110][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:35:21.110][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.110][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.110][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:35:21.110][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:35:21.110][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.110][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.110][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:35:21.110][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:35:21.110][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.110][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.110][ef$get] Asked field names are: formula.
biodb.TRACE[2022-03-17 18:35:21.126][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-03-17 18:35:21.126][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.126][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.126][ef$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:35:21.126][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:21.126][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.126][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.126][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:21.126][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:21.126][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.126][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.126][private$organizeFieldsByGroups] Groups [2]: "c("accession", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2022-03-17 18:35:21.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:21.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:21.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:21.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:21.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:21.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:21.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.141][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:35:21.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:35:21.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.141][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:35:21.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:35:21.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.141][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:35:21.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:35:21.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.157][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:35:21.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:35:21.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.157][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:35:21.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:35:21.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.157][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:35:21.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:35:21.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.157][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:35:21.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:35:21.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.157][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:35:21.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:35:21.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.173][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:35:21.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:35:21.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.173][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-03-17 18:35:21.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-03-17 18:35:21.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.173][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-03-17 18:35:21.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-03-17 18:35:21.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.173][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-03-17 18:35:21.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-03-17 18:35:21.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.188][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:35:21.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:21.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.188][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:35:21.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:21.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.188][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:35:21.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:21.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.188][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:21.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:21.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.188][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:21.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:21.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.204][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:21.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:21.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.204][private$entriesToListOfDataframes] Entry converted to data frame: [1, 7]: [accession, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, ...] [LMFA00000001, 10930192, 2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride, 626.491025, C40H66O5, ...].
biodb.DEBUG[2022-03-17 18:35:21.204][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-03-17 18:35:21.204][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:21.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:21.220][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:21.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:21.220][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:21.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-03-17 18:35:21.235][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-03-17 18:35:21.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-03-17 18:35:21.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.235][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-03-17 18:35:21.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-03-17 18:35:21.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.235][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-03-17 18:35:21.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-03-17 18:35:21.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.235][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-03-17 18:35:21.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-03-17 18:35:21.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.235][private$selectFields] Fields none
biodb.TRACE[2022-03-17 18:35:21.235][private$selectFields]
biodb.TRACE[2022-03-17 18:35:21.251][private$selectFields] Fields is null: TRUE
biodb.TRACE[2022-03-17 18:35:21.251][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-03-17 18:35:21.251][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:35:21.251][ef$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:21.251][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:21.251][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.251][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.251][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-03-17 18:35:21.251][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-03-17 18:35:21.251][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.251][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.251][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:35:21.251][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:35:21.251][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.251][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.251][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:35:21.251][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:35:21.266][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.266][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.266][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:35:21.266][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:35:21.266][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.266][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.266][ef$get] Asked field names are: formula.
biodb.TRACE[2022-03-17 18:35:21.266][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-03-17 18:35:21.266][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.266][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.266][ef$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:35:21.266][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:21.266][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.266][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.266][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:21.266][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:21.266][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.266][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.282][ef$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:21.282][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:21.282][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.282][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.282][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-03-17 18:35:21.282][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-03-17 18:35:21.282][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.282][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.282][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:35:21.282][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:35:21.282][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.282][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.282][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:35:21.282][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:35:21.282][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.282][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.282][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:35:21.282][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:35:21.282][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.298][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.298][ef$get] Asked field names are: formula.
biodb.TRACE[2022-03-17 18:35:21.298][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-03-17 18:35:21.298][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.298][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.298][ef$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:35:21.298][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:21.298][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.298][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.298][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:21.298][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:21.298][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.298][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.298][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:35:21.298][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-03-17 18:35:21.298][ef$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:21.298][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:21.298][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.298][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.313][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-03-17 18:35:21.313][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-03-17 18:35:21.313][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.313][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.313][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:35:21.313][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:35:21.313][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.313][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.313][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:35:21.313][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:35:21.313][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.313][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.313][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:35:21.313][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:35:21.313][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.313][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.313][ef$get] Asked field names are: formula.
biodb.TRACE[2022-03-17 18:35:21.329][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-03-17 18:35:21.329][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.329][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.329][ef$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:35:21.329][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:21.329][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.329][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.329][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:21.329][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:21.329][ef$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.329][ef$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.329][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2022-03-17 18:35:21.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:21.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:21.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:21.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:21.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-03-17 18:35:21.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-03-17 18:35:21.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.345][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-03-17 18:35:21.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-03-17 18:35:21.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.345][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-03-17 18:35:21.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-03-17 18:35:21.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.345][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-03-17 18:35:21.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-03-17 18:35:21.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.360][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:35:21.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:35:21.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.360][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:35:21.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:35:21.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.360][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:35:21.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-03-17 18:35:21.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.360][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:35:21.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:35:21.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.360][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:35:21.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:35:21.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.376][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:35:21.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-03-17 18:35:21.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.376][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:35:21.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:35:21.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.376][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:35:21.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:35:21.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.376][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:35:21.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-03-17 18:35:21.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.391][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-03-17 18:35:21.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-03-17 18:35:21.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.391][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-03-17 18:35:21.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-03-17 18:35:21.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.391][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-03-17 18:35:21.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-03-17 18:35:21.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.391][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:35:21.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:21.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.407][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:35:21.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:21.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.407][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-03-17 18:35:21.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-03-17 18:35:21.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.407][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:21.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:21.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.407][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:21.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:21.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.407][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:21.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-03-17 18:35:21.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-03-17 18:35:21.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-03-17 18:35:21.423][private$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[2022-03-17 18:35:21.423][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2022-03-17 18:35:21.423][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2022-03-17 18:35:21.423][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-03-17 18:35:21.423][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2022-03-17 18:35:21.423][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2022-03-17 18:35:21.423][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-03-17 18:35:21.423][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-03-17 18:35:21.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-03-17 18:35:21.423][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-03-17 18:35:21.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-03-17 18:35:21.438][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-03-17 18:35:21.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 167 ]
>
> proc.time()
user system elapsed
27.71 1.78 66.01
biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings
| name | user | system | elapsed | |
| LipidmapsStructureConn | 1.71 | 1.05 | 2.75 | |
| LipidmapsStructureEntry | 0.4 | 0.0 | 0.4 | |