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This page was generated on 2023-01-29 16:33:36 -0000 (Sun, 29 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch64R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" 4021
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CHECK results for biodbChebi on kunpeng1


To the developers/maintainers of the biodbChebi package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbChebi.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 178/2162HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbChebi 1.5.0  (landing page)
Pierrick Roger
Snapshot Date: 2023-01-27 13:09:27 -0000 (Fri, 27 Jan 2023)
git_url: https://git.bioconductor.org/packages/biodbChebi
git_branch: master
git_last_commit: b300c94
git_last_commit_date: 2022-11-01 15:25:43 -0000 (Tue, 01 Nov 2022)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    OK    WARNINGS  

Summary

Package: biodbChebi
Version: 1.5.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings biodbChebi_1.5.0.tar.gz
StartedAt: 2023-01-28 18:24:36 -0000 (Sat, 28 Jan 2023)
EndedAt: 2023-01-28 18:29:00 -0000 (Sat, 28 Jan 2023)
EllapsedTime: 264.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: biodbChebi.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings biodbChebi_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/biodbChebi.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.5.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... WARNING
Error in library(biodbChebi, lib.loc = "/home/biocbuild/bbs-3.17-bioc/R/library") : 
  there is no package called ‘biodbChebi’
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* 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 ... SKIPPED
* 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 ...
  ‘biodbChebi.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/biodbChebi.Rcheck/00check.log’
for details.

Installation output

biodbChebi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL biodbChebi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘biodbChebi’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbChebi)

Tests output

biodbChebi.Rcheck/tests/testthat.Rout


R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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

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

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

> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2023-01-28 18:25:29.256][biodb::testContext]
biodb.INFO [2023-01-28 18:25:29.259][biodb::testContext] ********************************************************************************
biodb.INFO [2023-01-28 18:25:29.260][biodb::testContext] Test context - Generic tests
biodb.INFO [2023-01-28 18:25:29.261][biodb::testContext] ********************************************************************************
biodb.INFO [2023-01-28 18:25:29.263][biodb::testContext]
biodb.INFO [2023-01-28 18:25:29.284][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-01-28 18:25:29.287][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-01-28 18:25:29.298][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-01-28 18:25:29.300][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-01-28 18:25:29.301][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-01-28 18:25:29.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:29.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:29.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:29.307][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-01-28 18:25:29.334][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-01-28 18:25:29.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:29.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:29.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:29.340][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-01-28 18:25:29.341][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-01-28 18:25:29.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:29.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:29.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:29.346][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-01-28 18:25:29.348][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-01-28 18:25:29.349][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-01-28 18:25:29.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:29.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:29.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:29.354][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-01-28 18:25:29.356][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-01-28 18:25:29.357][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-01-28 18:25:29.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:29.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:29.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:29.363][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-01-28 18:25:29.364][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-01-28 18:25:29.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:29.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:29.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:29.369][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-01-28 18:25:29.371][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-01-28 18:25:29.372][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-01-28 18:25:29.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:29.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:29.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:29.378][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-01-28 18:25:29.379][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-01-28 18:25:29.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:29.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:29.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:29.384][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-01-28 18:25:29.386][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-01-28 18:25:29.387][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-01-28 18:25:29.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:29.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:29.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:29.392][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-01-28 18:25:29.394][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-01-28 18:25:29.395][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-01-28 18:25:29.397][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-01-28 18:25:29.398][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-01-28 18:25:29.400][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-01-28 18:25:29.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:29.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:29.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:29.405][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-01-28 18:25:29.406][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-01-28 18:25:29.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:29.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:29.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:29.411][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-01-28 18:25:29.413][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-01-28 18:25:29.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:29.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:29.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:29.418][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-01-28 18:25:29.419][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-01-28 18:25:29.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:29.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:29.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:29.424][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-01-28 18:25:29.426][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-01-28 18:25:29.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:29.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:29.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:29.431][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-01-28 18:25:29.432][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-01-28 18:25:29.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:29.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:29.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:29.438][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-01-28 18:25:29.439][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-01-28 18:25:29.443][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-01-28 18:25:29.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:29.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:29.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:29.449][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-01-28 18:25:29.450][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-01-28 18:25:29.452][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-01-28 18:25:29.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:29.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:29.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:29.461][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-01-28 18:25:29.520][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-01-28 18:25:29.543][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-01-28 18:25:29.545][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-01-28 18:25:29.546][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-01-28 18:25:29.548][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-01-28 18:25:29.549][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-01-28 18:25:29.550][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-01-28 18:25:29.551][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-01-28 18:25:29.553][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-01-28 18:25:29.554][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-01-28 18:25:29.555][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-01-28 18:25:29.557][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-01-28 18:25:29.558][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-01-28 18:25:29.559][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:25:29.561][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-01-28 18:25:29.562][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-01-28 18:25:29.562][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-01-28 18:25:29.562][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-01-28 18:25:29.562][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-01-28 18:25:29.562][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-01-28 18:25:29.563][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-01-28 18:25:29.565][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:25:29.566][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:25:29.567][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-01-28 18:25:29.568][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:25:29.570][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:25:29.571][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-01-28 18:25:29.572][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:25:29.573][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-01-28 18:25:29.575][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-01-28 18:25:29.576][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-01-28 18:25:29.577][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:25:29.579][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-01-28 18:25:29.581][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-01-28 18:25:29.583][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-01-28 18:25:29.584][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-01-28 18:25:29.585][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-01-28 18:25:29.587][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-01-28 18:25:29.588][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-01-28 18:25:29.589][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-01-28 18:25:29.591][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-01-28 18:25:29.592][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-01-28 18:25:29.593][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-01-28 18:25:29.595][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-01-28 18:25:29.596][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-01-28 18:25:29.597][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-01-28 18:25:29.599][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:25:29.600][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-01-28 18:25:29.601][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-01-28 18:25:29.601][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-01-28 18:25:29.601][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-01-28 18:25:29.601][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-01-28 18:25:29.601][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-01-28 18:25:29.603][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-01-28 18:25:29.604][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:25:29.605][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:25:29.606][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-01-28 18:25:29.608][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:25:29.609][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:25:29.610][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-01-28 18:25:29.612][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:25:29.613][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-01-28 18:25:29.614][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-01-28 18:25:29.615][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-01-28 18:25:29.617][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:25:29.618][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-01-28 18:25:29.621][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-01-28 18:25:29.622][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-01-28 18:25:29.623][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-01-28 18:25:29.625][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-01-28 18:25:29.626][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-01-28 18:25:29.627][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-01-28 18:25:29.629][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-01-28 18:25:29.630][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-01-28 18:25:29.631][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-01-28 18:25:29.633][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-01-28 18:25:29.634][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-01-28 18:25:29.635][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-01-28 18:25:29.637][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-01-28 18:25:29.638][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:25:29.639][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-01-28 18:25:29.641][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:25:29.642][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-01-28 18:25:29.643][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:25:29.645][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:25:29.646][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-01-28 18:25:29.647][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:25:29.648][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:25:29.650][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-01-28 18:25:29.651][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:25:29.652][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-01-28 18:25:29.654][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-01-28 18:25:29.655][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-01-28 18:25:29.656][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:25:29.658][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-01-28 18:25:29.660][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-01-28 18:25:29.662][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-01-28 18:25:29.663][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-01-28 18:25:29.664][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-01-28 18:25:29.666][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-01-28 18:25:29.667][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-01-28 18:25:29.668][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-01-28 18:25:29.670][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-01-28 18:25:29.671][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-01-28 18:25:29.672][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-01-28 18:25:29.674][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-01-28 18:25:29.675][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-01-28 18:25:29.676][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-01-28 18:25:29.678][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:25:29.679][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-01-28 18:25:29.680][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:25:29.682][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-01-28 18:25:29.683][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:25:29.684][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:25:29.685][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-01-28 18:25:29.687][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:25:29.688][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:25:29.689][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-01-28 18:25:29.691][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:25:29.692][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-01-28 18:25:29.693][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-01-28 18:25:29.694][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-01-28 18:25:29.696][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:25:29.701][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-01-28 18:25:29.702][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:29.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:29.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:29.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:29.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:29.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:29.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:29.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:29.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:29.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:29.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:29.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:29.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:29.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:29.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:29.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:29.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:29.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:29.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:29.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:29.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:29.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:29.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:29.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:29.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:29.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:29.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:29.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:29.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:29.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:29.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:29.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:29.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:29.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:29.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:29.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:29.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:29.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:29.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:29.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:29.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:29.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:29.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:29.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:29.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:29.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:29.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:29.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:29.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:29.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:29.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:29.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:29.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:29.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:29.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:29.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:29.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:29.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:29.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:29.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:29.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:29.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:29.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:29.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:29.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:29.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:29.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:29.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:29.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:29.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:29.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:29.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:29.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:29.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:29.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:29.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:29.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:29.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:29.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:29.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:29.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:29.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:29.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:29.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:29.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:29.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:29.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:29.872][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-01-28 18:25:29.878][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-01-28 18:25:29.880][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-01-28 18:25:29.882][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-01-28 18:25:29.884][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-01-28 18:25:29.886][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-01-28 18:25:29.888][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-01-28 18:25:29.890][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-01-28 18:25:29.892][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-01-28 18:25:29.894][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-01-28 18:25:29.895][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-01-28 18:25:29.897][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-01-28 18:25:29.899][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-01-28 18:25:29.901][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-01-28 18:25:29.903][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-01-28 18:25:29.905][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-01-28 18:25:29.907][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-01-28 18:25:29.909][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-01-28 18:25:29.911][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-01-28 18:25:29.913][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-01-28 18:25:29.915][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-01-28 18:25:29.917][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-01-28 18:25:29.918][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-01-28 18:25:29.920][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-01-28 18:25:29.922][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-01-28 18:25:29.924][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-01-28 18:25:29.926][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-01-28 18:25:29.944][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-01-28 18:25:29.946][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-01-28 18:25:29.948][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-01-28 18:25:29.950][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-01-28 18:25:29.952][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-01-28 18:25:29.954][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-01-28 18:25:29.955][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-01-28 18:25:29.957][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-01-28 18:25:29.975][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-01-28 18:25:29.977][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-01-28 18:25:29.979][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-01-28 18:25:29.981][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-01-28 18:25:29.983][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-01-28 18:25:29.985][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-01-28 18:25:29.987][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-01-28 18:25:29.988][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-01-28 18:25:29.990][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-01-28 18:25:30.009][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-01-28 18:25:30.011][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-01-28 18:25:30.012][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-01-28 18:25:30.014][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-01-28 18:25:30.016][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-01-28 18:25:30.018][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-01-28 18:25:30.020][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-01-28 18:25:30.022][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-01-28 18:25:30.040][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-01-28 18:25:30.042][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-01-28 18:25:30.044][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-01-28 18:25:30.046][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-01-28 18:25:30.048][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-01-28 18:25:30.049][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-01-28 18:25:30.051][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-01-28 18:25:30.053][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-01-28 18:25:30.068][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-01-28 18:25:30.070][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-01-28 18:25:30.072][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-01-28 18:25:30.074][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-01-28 18:25:30.095][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-01-28 18:25:30.097][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-01-28 18:25:30.099][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-01-28 18:25:30.101][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-01-28 18:25:30.103][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-01-28 18:25:30.105][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-01-28 18:25:30.106][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-01-28 18:25:30.108][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-01-28 18:25:30.110][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-01-28 18:25:30.115][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-01-28 18:25:30.122][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-01-28 18:25:30.125][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-01-28 18:25:30.127][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-01-28 18:25:30.129][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-01-28 18:25:30.131][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-01-28 18:25:30.132][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-01-28 18:25:30.134][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-01-28 18:25:30.136][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-01-28 18:25:30.138][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-01-28 18:25:30.146][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-01-28 18:25:30.148][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-01-28 18:25:30.152][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-01-28 18:25:30.154][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:30.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:30.156][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:30.157][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[2023-01-28 18:25:30.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:30.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:25:30.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:25:30.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:30.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:30.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:30.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:30.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:30.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:25:30.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:25:30.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:30.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:30.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:30.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:30.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:30.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:25:30.184][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:25:30.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:30.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:30.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:30.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:30.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:30.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:25:30.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:25:30.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:30.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:30.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:30.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:30.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:30.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:25:30.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:25:30.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:30.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:30.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:30.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:30.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:30.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:25:30.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:25:30.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:30.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:30.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:30.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:30.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:30.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:25:30.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:25:30.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:30.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:30.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:30.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:30.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:30.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:25:30.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:25:30.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:30.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:30.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:30.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:30.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:30.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:25:30.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:25:30.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:30.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:30.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:30.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:30.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:30.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:25:30.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:25:30.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:30.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:30.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:30.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:30.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:30.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:25:30.253][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:25:30.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:30.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:30.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:30.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:30.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:30.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:25:30.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:25:30.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:30.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:30.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:30.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:30.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:30.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:25:30.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:25:30.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:30.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:30.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:30.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:30.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:30.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:25:30.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:25:30.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:30.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:30.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:30.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:30.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:30.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:25:30.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:25:30.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:30.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:30.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:30.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:30.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:30.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:25:30.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:25:30.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:30.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:30.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:30.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:30.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:25:30.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:25:30.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:25:30.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:30.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:30.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:30.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:30.319][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-01-28 18:25:30.333][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-01-28 18:25:30.335][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-01-28 18:25:30.337][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-01-28 18:25:30.338][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-01-28 18:25:30.339][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-01-28 18:25:30.341][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-01-28 18:25:30.342][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-01-28 18:25:30.343][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-01-28 18:25:30.345][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-01-28 18:25:30.346][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-01-28 18:25:30.347][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-01-28 18:25:30.349][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-01-28 18:25:30.350][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-01-28 18:25:30.351][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-01-28 18:25:30.352][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-01-28 18:25:30.352][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-01-28 18:25:30.352][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-01-28 18:25:30.352][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-01-28 18:25:30.352][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-01-28 18:25:30.352][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-01-28 18:25:30.352][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-01-28 18:25:30.352][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-01-28 18:25:30.352][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-01-28 18:25:30.352][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-01-28 18:25:30.352][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-01-28 18:25:30.354][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-01-28 18:25:30.356][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-01-28 18:25:30.356][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-01-28 18:25:30.356][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-01-28 18:25:30.357][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-01-28 18:25:30.358][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:25:30.359][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:25:30.361][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-01-28 18:25:30.362][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:25:30.363][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:25:30.365][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-01-28 18:25:30.366][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-01-28 18:25:30.366][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-01-28 18:25:30.367][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-01-28 18:25:30.368][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-01-28 18:25:30.370][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-01-28 18:25:30.371][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-01-28 18:25:30.371][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-01-28 18:25:30.379][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-01-28 18:25:30.381][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-01-28 18:25:30.384][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-01-28 18:25:30.386][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-01-28 18:25:30.388][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-01-28 18:25:30.390][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-01-28 18:25:30.422][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-01-28 18:25:30.423][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-01-28 18:25:30.429][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-01-28 18:25:30.435][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-01-28 18:25:30.441][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-01-28 18:25:30.443][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-01-28 18:25:30.445][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-01-28 18:25:30.446][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-01-28 18:25:30.467][biodb::testThat]
biodb.INFO [2023-01-28 18:25:30.469][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2023-01-28 18:25:30.470][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-01-28 18:25:30.471][biodb::testThat]
biodb.TRACE[2023-01-28 18:25:30.477][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2023-01-28 18:25:30.483][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-01-28 18:25:30.488][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-01-28 18:25:30.499][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:25:30.501][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:25:30.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:25:30.519][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:30.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:30.522][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:30.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:25:30.539][ef$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:30.541][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:30.542][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:30.544][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:30.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:30.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:30.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:30.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:30.573][ef$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:25:30.574][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:25:30.576][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:30.577][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:30.630][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:25:30.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:25:30.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:30.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:30.639][ef$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:25:30.641][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:25:30.642][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:30.643][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:30.645][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:25:30.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:25:30.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:30.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:30.655][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:25:30.656][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:25:30.658][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:30.659][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:30.661][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:25:30.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:25:30.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:30.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:30.670][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:25:30.671][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:25:30.673][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:30.674][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:30.676][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:25:30.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:25:30.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:30.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:30.685][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:25:30.686][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:25:30.688][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:30.689][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:30.691][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:25:30.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:25:30.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:30.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:30.700][ef$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:25:30.702][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:30.703][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:30.704][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:30.706][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:25:30.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:30.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:30.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:30.715][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:25:30.717][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:25:30.718][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:30.720][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:30.722][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:25:30.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:25:30.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:30.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:30.731][ef$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:25:30.733][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:25:30.734][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:30.735][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:30.737][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:25:30.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:25:30.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:30.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:30.747][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:25:30.748][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:25:30.750][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:30.751][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:30.753][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:25:30.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:25:30.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:30.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:30.762][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:25:30.763][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:25:30.765][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:30.766][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:30.768][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:25:30.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:25:30.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:30.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:30.777][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:25:30.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:25:30.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:30.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:30.783][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:25:30.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:25:30.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:30.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:30.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:30.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:30.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:30.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:30.794][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:25:30.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:25:30.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:30.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:30.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:30.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:30.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:30.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:30.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:30.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:30.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:30.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:30.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:30.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:30.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:30.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:30.882][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:30.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:30.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:30.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:30.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:30.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:30.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:30.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:30.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:30.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:30.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:30.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:25:30.898][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2023-01-28 18:25:30.905][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:25:30.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:25:30.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:30.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:30.953][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:25:30.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:25:30.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:30.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:30.991][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:25:30.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:25:30.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:30.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:30.996][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:25:30.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:25:30.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.002][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:31.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:31.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.007][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:31.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:31.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.012][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-01-28 18:25:31.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-01-28 18:25:31.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.017][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-01-28 18:25:31.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-01-28 18:25:31.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.023][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-01-28 18:25:31.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-01-28 18:25:31.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.028][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-01-28 18:25:31.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-01-28 18:25:31.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:31.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:31.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.078][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:25:31.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:25:31.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.091][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:31.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:31.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:31.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:31.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:31.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:31.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:31.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:31.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.116][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:31.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:31.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:31.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:31.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.127][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:25:31.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:25:31.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.133][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:25:31.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:25:31.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.138][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:25:31.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:25:31.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:31.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:31.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:31.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:31.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:31.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:31.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.174][ef$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:31.176][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:31.177][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.178][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:31.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:31.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.195][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:25:31.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:25:31.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.202][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:25:31.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:25:31.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.208][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:25:31.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:25:31.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.214][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:25:31.221][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:25:31.223][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.224][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.226][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:25:31.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:25:31.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.250][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:25:31.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:25:31.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.256][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:25:31.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:25:31.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.262][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:25:31.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:25:31.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.268][ef$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:25:31.270][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:25:31.271][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.272][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.274][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:25:31.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:25:31.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.291][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:25:31.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:25:31.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.297][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:25:31.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:25:31.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.303][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:25:31.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:25:31.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.308][ef$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:25:31.310][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:25:31.311][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.312][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.314][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:25:31.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:25:31.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.329][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:31.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:31.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.336][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:31.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:31.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.341][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:31.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:31.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.347][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:31.349][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:31.350][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.352][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.353][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:31.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:31.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.369][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:25:31.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:25:31.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.376][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:25:31.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:25:31.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.381][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:25:31.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:25:31.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.387][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:25:31.389][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:25:31.390][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.392][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.393][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:25:31.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:25:31.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.409][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:25:31.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:25:31.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.416][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:25:31.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:25:31.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.422][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:25:31.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:25:31.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.428][ef$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:25:31.429][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:25:31.431][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.432][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.433][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:25:31.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:25:31.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.450][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-01-28 18:25:31.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:25:31.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.456][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-01-28 18:25:31.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:25:31.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.462][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-01-28 18:25:31.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:25:31.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.468][ef$get] Asked field names are: n.stars.
biodb.TRACE[2023-01-28 18:25:31.470][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:25:31.471][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.473][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.474][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-01-28 18:25:31.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:25:31.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.492][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:25:31.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:25:31.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.499][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:25:31.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:25:31.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.505][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:25:31.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:25:31.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.511][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:25:31.512][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:25:31.514][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.515][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.516][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:25:31.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:25:31.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.551][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:25:31.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:25:31.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.557][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:25:31.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:25:31.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.563][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:25:31.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:25:31.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.568][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:25:31.569][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:25:31.571][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.572][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.573][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:25:31.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:25:31.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.589][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:25:31.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:25:31.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.595][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:25:31.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:25:31.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.600][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:25:31.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:25:31.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.606][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:25:31.607][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:25:31.608][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.610][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.611][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:25:31.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:25:31.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.626][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:25:31.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:25:31.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.632][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:25:31.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:25:31.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.637][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:25:31.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:25:31.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.642][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:25:31.644][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:25:31.645][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.646][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.648][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:25:31.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:25:31.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.663][ef$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:31.665][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:31.666][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.667][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.675][ef$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:25:31.676][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:25:31.678][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.679][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.687][ef$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:25:31.688][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:25:31.690][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.691][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.699][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:25:31.700][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:25:31.702][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.703][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.711][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:25:31.712][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:25:31.714][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.715][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.723][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:25:31.724][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:25:31.726][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.727][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.734][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:31.736][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:31.737][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.739][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.746][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:25:31.748][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:25:31.749][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.751][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.759][ef$get] Asked field names are: n.stars.
biodb.TRACE[2023-01-28 18:25:31.760][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:25:31.762][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.763][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.771][ef$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:25:31.772][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:25:31.774][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.775][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.783][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:25:31.784][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:25:31.786][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.787][ef$get] fields variable is a list.
biodb.INFO [2023-01-28 18:25:31.796][biodb::testThat]
biodb.INFO [2023-01-28 18:25:31.797][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-01-28 18:25:31.798][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-01-28 18:25:31.800][biodb::testThat]
biodb.DEBUG[2023-01-28 18:25:31.827][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2023-01-28 18:25:31.837][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-01-28 18:25:31.855][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2023-01-28 18:25:31.860][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-01-28 18:25:31.863][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2023-01-28 18:25:31.865][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-01-28 18:25:31.943][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-01-28 18:25:31.944][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-01-28 18:25:31.946][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:25:31.948][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:25:31.949][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:25:31.958][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:31.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:31.960][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:31.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:25:31.965][ef$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:31.966][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:31.968][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.969][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:31.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:31.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:31.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:31.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:32.003][ef$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:25:32.005][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:25:32.006][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:32.007][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:32.009][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:25:32.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:25:32.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:32.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:32.018][ef$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:25:32.020][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:25:32.021][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:32.022][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:32.024][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:25:32.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:25:32.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:32.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:32.033][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:25:32.035][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:25:32.036][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:32.038][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:32.039][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:25:32.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:25:32.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:32.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:32.048][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:25:32.050][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:25:32.051][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:32.052][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:32.054][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:25:32.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:25:32.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:32.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:32.064][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:25:32.065][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:25:32.066][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:32.068][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:32.069][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:25:32.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:25:32.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:32.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:32.078][ef$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:25:32.080][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:32.081][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:32.082][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:32.084][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:25:32.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:32.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:32.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:32.093][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:25:32.095][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:25:32.096][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:32.097][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:32.099][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:25:32.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:25:32.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:32.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:32.108][ef$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:25:32.109][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:25:32.111][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:32.112][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:32.114][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:25:32.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:25:32.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:32.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:32.132][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:25:32.134][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:25:32.135][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:32.137][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:32.138][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:25:32.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:25:32.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:32.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:32.147][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:25:32.149][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:25:32.150][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:32.151][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:32.153][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:25:32.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:25:32.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:32.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:32.162][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:25:32.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:25:32.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:32.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:32.168][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:25:32.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:25:32.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:32.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:32.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:32.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:32.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:32.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:32.179][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:25:32.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:25:32.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:32.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:32.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:32.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:32.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:32.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:32.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:32.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:32.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:32.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:32.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:32.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:32.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:32.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:32.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:32.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:32.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:32.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:32.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:32.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:32.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:32.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:32.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:32.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:32.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:32.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:25:32.223][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2023-01-28 18:25:32.224][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-01-28 18:25:32.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-01-28 18:25:32.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:32.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:32.230][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-01-28 18:25:32.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-01-28 18:25:32.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:32.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:32.236][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-01-28 18:25:32.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-01-28 18:25:32.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:32.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-01-28 18:25:32.249][biodb::testThat]
biodb.INFO [2023-01-28 18:25:32.250][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2023-01-28 18:25:32.252][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-01-28 18:25:32.253][biodb::testThat]
biodb.TRACE[2023-01-28 18:25:32.257][ef$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:25:32.259][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:25:32.260][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:32.261][ef$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:25:32.263][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2023-01-28 18:25:32.302][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:25:32.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:25:32.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:32.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:32.307][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:25:32.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:25:32.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:32.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:32.312][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:25:32.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:25:32.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:32.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:25:32.320][function(conn, opt)] With value "squalene".
biodb.DEBUG[2023-01-28 18:25:32.336][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-01-28 18:25:32.364][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-01-28 18:25:32.394][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2023-01-28 18:25:32.396][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-01-28 18:25:32.402][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2023-01-28 18:25:32.434][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:25:32.439][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:25:32.440][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:25:32.442][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-01-28 18:25:35.406][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-01-28 18:25:36.730][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:25:36.756][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2023-01-28 18:25:36.806][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2023-01-28 18:25:36.829][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2023-01-28 18:25:36.865][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:25:36.867][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:25:36.868][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:36.870][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:36.871][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:36.872][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:36.874][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:36.891][ef$get] fields variable is a list.
biodb.INFO [2023-01-28 18:25:36.894][biodb::testThat]
biodb.INFO [2023-01-28 18:25:36.895][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2023-01-28 18:25:36.897][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-01-28 18:25:36.898][biodb::testThat]
biodb.TRACE[2023-01-28 18:25:36.990][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:25:36.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:25:36.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:36.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:36.995][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:25:36.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:25:36.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:36.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:37.000][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:25:37.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:25:37.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:37.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:25:37.200][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:25:37.221][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-01-28 18:25:37.223][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-01-28 18:25:37.225][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-01-28 18:25:37.226][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2023-01-28 18:25:37.265][biodb::testThat]
biodb.INFO [2023-01-28 18:25:37.266][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2023-01-28 18:25:37.268][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-01-28 18:25:37.269][biodb::testThat]
biodb.TRACE[2023-01-28 18:25:37.354][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:25:37.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:25:37.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:37.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:37.359][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:25:37.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:25:37.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:37.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:37.365][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:25:37.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:25:37.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:37.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:37.370][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:25:37.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:25:37.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:37.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:37.376][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:37.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:37.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:37.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:37.382][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:37.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:37.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:37.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:37.388][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-01-28 18:25:37.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-01-28 18:25:37.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:37.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:37.393][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-01-28 18:25:37.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-01-28 18:25:37.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:37.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:37.398][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-01-28 18:25:37.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-01-28 18:25:37.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:37.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:37.404][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-01-28 18:25:37.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-01-28 18:25:37.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:37.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:37.438][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:25:37.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:25:37.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:37.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:37.444][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:25:37.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:25:37.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:37.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:37.458][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:25:37.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:25:37.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:37.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:37.463][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:25:37.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:25:37.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:37.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:37.468][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:37.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:37.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:37.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:37.474][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:37.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:37.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:37.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:37.480][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-01-28 18:25:37.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-01-28 18:25:37.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:37.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:37.485][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-01-28 18:25:37.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-01-28 18:25:37.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:37.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:37.491][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-01-28 18:25:37.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-01-28 18:25:37.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:37.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:37.496][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-01-28 18:25:37.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-01-28 18:25:37.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:37.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-01-28 18:25:37.506][biodb::testThat]
biodb.INFO [2023-01-28 18:25:37.507][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-01-28 18:25:37.508][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-01-28 18:25:37.510][biodb::testThat]
biodb.INFO [2023-01-28 18:25:37.517][biodb::testThat]
biodb.INFO [2023-01-28 18:25:37.518][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-01-28 18:25:37.519][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-01-28 18:25:37.521][biodb::testThat]
biodb.INFO [2023-01-28 18:25:37.528][biodb::testThat]
biodb.INFO [2023-01-28 18:25:37.529][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2023-01-28 18:25:37.530][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-01-28 18:25:37.532][biodb::testThat]
biodb.DEBUG[2023-01-28 18:25:37.536][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2023-01-28 18:25:38.740][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2023-01-28 18:25:41.545][biodb::testThat]
biodb.INFO [2023-01-28 18:25:41.547][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2023-01-28 18:25:41.548][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-01-28 18:25:41.549][biodb::testThat]
biodb.DEBUG[2023-01-28 18:25:42.815][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=15440&dimensions=400.
biodb.TRACE[2023-01-28 18:25:43.989][ef$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:25:44.007][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:25:44.008][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:44.010][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:44.012][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:25:44.013][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:25:44.015][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:44.016][ef$get] fields variable is a list.
biodb.INFO [2023-01-28 18:25:44.019][biodb::testThat]
biodb.INFO [2023-01-28 18:25:44.020][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2023-01-28 18:25:44.022][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-01-28 18:25:44.039][biodb::testThat]
biodb.TRACE[2023-01-28 18:25:44.081][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:25:44.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:25:44.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:44.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:44.086][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:25:44.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:25:44.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:44.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:44.108][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:25:44.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:25:44.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:44.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:25:44.382][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.INFO [2023-01-28 18:25:44.387][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.DEBUG[2023-01-28 18:25:44.417][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:25:44.418][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:25:44.441][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-01-28 18:25:45.711][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-01-28 18:25:47.039][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:25:47.073][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2023-01-28 18:25:47.107][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2023-01-28 18:25:47.300][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:25:47.321][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-01-28 18:25:47.323][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-01-28 18:25:47.324][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-01-28 18:25:47.326][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2023-01-28 18:25:47.365][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-01-28 18:25:47.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-01-28 18:25:47.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:47.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:47.417][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:47.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:47.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:47.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:47.423][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:47.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:47.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:47.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:47.445][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:47.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:47.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:47.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:47.476][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:47.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:47.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:47.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:47.482][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:47.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:47.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:47.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:25:47.562][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:25:47.567][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:25:47.568][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:25:47.570][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-01-28 18:25:48.734][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-01-28 18:25:49.944][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:25:49.955][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2023-01-28 18:25:49.971][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2023-01-28 18:25:49.978][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:25:49.980][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:25:49.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:25:49.989][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:49.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:49.992][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:49.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:49.995][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2023-01-28 18:25:50.077][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-01-28 18:25:50.079][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2023-01-28 18:25:50.081][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-01-28 18:25:50.083][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-01-28 18:25:50.085][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-01-28 18:25:50.086][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-01-28 18:25:50.088][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-01-28 18:25:50.089][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-01-28 18:25:50.093][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:25:50.094][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:25:50.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:25:50.104][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:50.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:50.106][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:50.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:25:50.109][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2023-01-28 18:25:50.129][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:25:50.131][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:25:50.133][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2023-01-28 18:25:51.320][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2023-01-28 18:25:52.497][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2023-01-28 18:25:52.502][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2023-01-28 18:25:52.524][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2023-01-28 18:25:52.555][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2023-01-28 18:25:52.585][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2023-01-28 18:25:52.591][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-01-28 18:25:52.645][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-01-28 18:25:52.646][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-01-28 18:25:52.649][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:25:52.650][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:25:52.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:25:52.675][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:52.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:52.678][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:52.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:25:52.682][ef$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:52.684][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:52.685][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:52.686][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:52.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:52.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:52.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:52.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:52.714][ef$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:25:52.715][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:25:52.717][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:52.718][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:52.736][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:25:52.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:25:52.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:52.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:52.746][ef$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:25:52.747][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:25:52.748][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:52.750][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:52.768][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:25:52.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:25:52.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:52.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:52.778][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:25:52.788][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:25:52.790][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:52.792][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:52.793][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:25:52.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:25:52.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:52.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:52.802][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:25:52.804][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:25:52.805][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:52.807][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:52.808][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:25:52.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:25:52.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:52.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:52.818][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:25:52.819][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:25:52.821][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:52.822][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:52.824][ef$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:25:52.825][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:52.826][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:52.828][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:52.830][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:25:52.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:52.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:52.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:52.839][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:25:52.841][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:25:52.842][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:52.843][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:52.845][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:25:52.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:25:52.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:52.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:52.855][ef$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:25:52.856][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:25:52.858][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:52.859][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:52.861][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:25:52.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:25:52.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:52.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:52.887][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:25:52.888][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:25:52.890][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:52.891][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:52.893][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:25:52.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:25:52.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:52.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:52.902][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:25:52.904][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:25:52.905][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:52.907][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:52.908][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:25:52.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:25:52.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:52.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:52.918][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:25:52.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:25:52.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:52.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:52.924][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:25:52.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:25:52.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:52.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:52.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:52.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:52.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:52.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:52.936][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:25:52.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:25:52.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:52.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:52.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:52.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:52.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:52.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:52.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:52.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:52.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:52.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:52.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:52.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:52.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:52.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:52.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:52.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:52.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:52.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:52.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:52.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:52.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:52.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:52.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:25:52.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:25:52.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:52.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:25:52.989][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2023-01-28 18:25:53.003][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:53.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:53.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:53.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:53.008][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:53.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:53.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:53.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:53.014][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:53.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:53.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:53.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:25:53.021][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:25:53.025][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:25:53.027][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:25:53.029][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-01-28 18:25:54.222][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-01-28 18:25:55.422][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:25:55.432][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2023-01-28 18:25:55.463][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2023-01-28 18:25:55.517][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:25:55.518][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:25:55.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:25:55.544][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:25:55.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:25:55.547][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:25:55.548][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.TRACE[2023-01-28 18:25:55.549][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:55.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:55.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:55.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:55.555][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:55.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:55.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:55.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:25:55.607][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:55.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:25:55.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:25:55.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:25:55.614][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:25:55.618][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:25:55.620][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:25:55.651][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-01-28 18:25:56.835][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-01-28 18:25:58.046][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:25:58.056][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content"
biodb.TRACE[2023-01-28 18:25:58.088][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.request"
biodb.DEBUG[2023-01-28 18:25:58.214][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:25:58.235][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:25:58.236][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:25:58.239][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-01-28 18:25:59.550][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-01-28 18:26:00.998][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:26:01.012][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2023-01-28 18:26:01.043][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2023-01-28 18:26:01.104][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:01.105][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:01.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:01.114][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:01.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:01.133][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:01.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:26:01.136][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:01.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:01.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:01.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:01.142][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:01.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:01.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:01.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:01.164][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:01.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:01.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:01.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:01.170][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:01.171][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:01.172][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:01.197][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:01.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:01.199][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:01.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:26:01.202][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2023-01-28 18:26:01.204][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-01-28 18:26:01.206][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2023-01-28 18:26:01.223][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-01-28 18:26:01.225][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-01-28 18:26:01.227][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-01-28 18:26:01.228][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-01-28 18:26:01.230][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-01-28 18:26:01.231][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-01-28 18:26:01.279][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:01.281][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:01.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:01.307][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:01.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:01.309][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:01.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:26:01.312][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2023-01-28 18:26:01.316][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:26:01.317][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:26:01.319][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2023-01-28 18:26:02.524][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2023-01-28 18:26:03.703][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:26:03.712][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2023-01-28 18:26:03.743][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2023-01-28 18:26:03.773][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2023-01-28 18:26:03.795][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-01-28 18:26:03.834][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-01-28 18:26:03.835][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-01-28 18:26:03.838][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:03.839][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:03.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:03.864][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:03.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:03.867][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:03.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:26:03.871][ef$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:03.873][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:03.874][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:03.891][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:03.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:03.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:03.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:03.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:03.902][ef$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:26:03.903][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:26:03.905][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:03.906][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:03.924][ef$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:26:03.926][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:26:03.927][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:03.928][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:03.930][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:26:03.931][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:26:03.933][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:03.934][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:03.936][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:26:03.937][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:26:03.938][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:03.956][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:03.958][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:26:03.959][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:26:03.960][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:03.961][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:03.963][ef$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:26:03.964][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:03.965][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:03.967][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:03.968][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:03.970][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:03.983][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:03.984][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:03.986][ef$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:26:03.988][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:26:03.989][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:03.990][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:03.992][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:26:03.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:26:03.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:03.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:04.001][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:26:04.002][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:26:04.004][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:04.005][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:04.007][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:26:04.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:26:04.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:04.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:04.027][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:26:04.029][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:26:04.030][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:04.031][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:04.033][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:04.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:04.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:04.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:04.038][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:04.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:04.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:04.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:04.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:04.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:04.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:04.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:04.049][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:04.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:04.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:04.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:04.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:04.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:04.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:04.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:04.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:04.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:04.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:04.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:04.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:04.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:04.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:04.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:04.075][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:04.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:04.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:04.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:04.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:04.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:04.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:04.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:04.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:04.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:04.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:04.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:04.091][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2023-01-28 18:26:04.093][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:04.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:04.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:04.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:04.098][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:04.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:04.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:04.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:04.104][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:04.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:04.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:04.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:04.109][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:04.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:04.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:04.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:04.115][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:04.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:04.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:04.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:04.121][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:04.122][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:04.123][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:04.131][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:04.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:04.134][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:04.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:26:04.137][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2023-01-28 18:26:04.138][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-01-28 18:26:04.140][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2023-01-28 18:26:04.142][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-01-28 18:26:04.144][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-01-28 18:26:04.145][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-01-28 18:26:04.147][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-01-28 18:26:04.148][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-01-28 18:26:04.149][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-01-28 18:26:04.153][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:04.154][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:04.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:04.164][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:04.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:04.166][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:04.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:26:04.169][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2023-01-28 18:26:04.173][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:26:04.174][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:26:04.176][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2023-01-28 18:26:06.345][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2023-01-28 18:26:07.574][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:26:07.585][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2023-01-28 18:26:07.616][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2023-01-28 18:26:07.647][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2023-01-28 18:26:07.656][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-01-28 18:26:07.695][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-01-28 18:26:07.696][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-01-28 18:26:07.699][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:07.700][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:07.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:07.725][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:07.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:07.728][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:07.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:26:07.732][ef$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:07.734][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:07.735][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:07.736][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:07.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:07.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:07.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:07.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:07.747][ef$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:26:07.749][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:26:07.750][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:07.751][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:07.753][ef$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:26:07.754][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:26:07.756][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:07.757][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:07.759][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:26:07.760][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:26:07.762][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:07.763][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:07.765][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:26:07.766][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:26:07.768][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:07.769][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:07.770][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:26:07.772][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:26:07.773][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:07.775][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:07.776][ef$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:26:07.778][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:07.779][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:07.780][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:07.782][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:07.783][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:07.785][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:07.786][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:07.788][ef$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:26:07.789][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:26:07.790][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:07.792][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:07.794][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:26:07.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:26:07.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:07.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:07.803][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:26:07.805][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:26:07.806][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:07.808][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:07.809][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:26:07.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:26:07.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:07.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:07.819][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:26:07.821][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:26:07.822][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:07.823][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:07.825][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:07.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:07.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:07.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:07.831][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:07.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:07.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:07.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:07.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:07.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:07.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:07.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:07.842][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:07.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:07.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:07.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:07.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:07.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:07.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:07.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:07.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:07.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:07.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:07.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:07.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:07.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:07.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:07.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:07.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:07.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:07.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:07.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:07.882][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:07.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:07.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:07.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:07.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:07.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:07.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:07.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:07.893][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2023-01-28 18:26:07.895][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:07.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:07.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:07.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:07.901][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:07.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:07.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:07.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:07.906][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:07.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:07.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:07.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:07.912][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:07.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:07.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:07.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:07.918][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:07.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:07.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:07.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:07.923][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:07.924][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:07.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:07.934][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:07.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:07.936][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:07.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:26:07.939][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2023-01-28 18:26:07.940][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-01-28 18:26:07.943][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2023-01-28 18:26:07.944][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-01-28 18:26:07.946][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-01-28 18:26:07.947][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-01-28 18:26:07.949][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-01-28 18:26:07.950][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-01-28 18:26:07.951][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-01-28 18:26:07.955][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:07.956][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:07.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:07.966][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:07.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:07.968][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:07.970][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[2023-01-28 18:26:07.971][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2023-01-28 18:26:07.975][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:26:07.976][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:26:07.978][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2023-01-28 18:26:09.137][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2023-01-28 18:26:10.413][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:26:10.424][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2023-01-28 18:26:10.521][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2023-01-28 18:26:10.572][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2023-01-28 18:26:10.578][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-01-28 18:26:10.622][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-01-28 18:26:10.625][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-01-28 18:26:10.627][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:10.629][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:10.630][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:10.640][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:10.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:10.643][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:10.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:26:10.648][ef$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:10.650][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:10.652][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:10.653][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:10.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:10.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:10.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:10.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:10.666][ef$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:26:10.668][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:26:10.670][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:10.671][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:10.673][ef$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:26:10.675][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:26:10.677][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:10.678][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:10.680][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:26:10.682][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:26:10.684][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:10.685][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:10.687][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:26:10.689][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:26:10.691][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:10.692][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:10.694][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:26:10.696][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:26:10.697][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:10.699][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:10.701][ef$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:26:10.702][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:10.704][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:10.705][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:10.707][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:10.708][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:10.710][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:10.711][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:10.713][ef$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:26:10.715][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:26:10.716][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:10.718][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:10.720][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:26:10.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:26:10.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:10.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:10.730][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:26:10.732][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:26:10.733][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:10.735][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:10.737][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:26:10.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:26:10.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:10.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:10.747][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:26:10.748][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:26:10.750][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:10.751][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:10.753][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:10.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:10.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:10.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:10.759][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:10.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:10.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:10.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:10.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:10.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:10.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:10.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:10.771][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:10.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:10.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:10.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:10.777][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:10.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:10.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:10.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:10.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:10.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:10.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:10.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:10.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:10.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:10.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:10.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:10.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:10.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:10.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:10.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:10.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:10.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:10.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:10.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:10.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:10.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:10.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:10.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:10.826][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2023-01-28 18:26:10.828][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:10.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:10.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:10.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:10.834][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:10.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:10.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:10.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:10.839][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:10.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:10.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:10.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:10.845][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:10.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:10.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:10.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:10.851][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:10.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:10.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:10.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:10.856][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:10.858][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:10.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:10.867][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:10.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:10.870][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:10.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:26:10.873][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2023-01-28 18:26:10.874][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-01-28 18:26:10.876][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2023-01-28 18:26:10.878][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-01-28 18:26:10.880][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-01-28 18:26:10.881][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-01-28 18:26:10.883][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-01-28 18:26:10.884][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-01-28 18:26:10.886][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-01-28 18:26:10.889][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:10.891][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:10.892][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:10.900][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:10.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:10.903][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:10.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:26:10.906][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2023-01-28 18:26:10.910][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:26:10.911][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:26:10.913][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2023-01-28 18:26:12.050][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2023-01-28 18:26:14.789][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:26:14.815][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2023-01-28 18:26:14.830][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2023-01-28 18:26:14.860][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2023-01-28 18:26:14.865][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-01-28 18:26:14.949][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-01-28 18:26:14.951][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-01-28 18:26:14.953][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:14.954][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:14.955][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:14.979][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:14.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:14.982][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:14.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:26:14.987][ef$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:14.988][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:14.989][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:14.991][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:14.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:14.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:15.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:15.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:15.018][ef$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:26:15.020][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:26:15.021][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:15.022][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:15.024][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:26:15.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:26:15.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:15.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:15.050][ef$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:26:15.051][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:26:15.053][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:15.054][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:15.056][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:26:15.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:26:15.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:15.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:15.082][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:26:15.083][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:26:15.085][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:15.086][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:15.088][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:26:15.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:26:15.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:15.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:15.099][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:26:15.100][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:26:15.102][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:15.103][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:15.105][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:26:15.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:26:15.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:15.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:15.130][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:26:15.132][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:26:15.134][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:15.135][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:15.137][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:26:15.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:26:15.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:15.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:15.163][ef$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:26:15.165][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:15.166][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:15.167][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:15.169][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:26:15.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:15.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:15.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:15.194][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:15.196][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:15.197][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:15.198][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:15.200][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:15.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:15.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:15.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:15.225][ef$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:26:15.226][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:26:15.228][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:15.229][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:15.231][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:26:15.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:26:15.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:15.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:15.260][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:26:15.262][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:26:15.263][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:15.264][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:15.266][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:26:15.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:26:15.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:15.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:15.295][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:26:15.297][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:26:15.298][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:15.299][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:15.301][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:26:15.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:26:15.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:15.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:15.339][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:15.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:15.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:15.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:15.344][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:15.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:15.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:15.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:15.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:15.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:15.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:15.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:15.356][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:15.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:15.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:15.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:15.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:15.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:15.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:15.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:15.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:15.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:15.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:15.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:15.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:15.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:15.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:15.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:15.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:15.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:15.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:15.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:15.397][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:15.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:15.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:15.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:15.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:15.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:15.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:15.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:15.408][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2023-01-28 18:26:15.409][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:15.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:15.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:15.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:15.415][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:15.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:15.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:15.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:15.421][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:15.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:15.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:15.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:15.426][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:15.427][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:15.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:15.437][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:15.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:15.439][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:15.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:26:15.442][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2023-01-28 18:26:15.444][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-01-28 18:26:15.446][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2023-01-28 18:26:15.448][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-01-28 18:26:15.449][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-01-28 18:26:15.451][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-01-28 18:26:15.452][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-01-28 18:26:15.454][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-01-28 18:26:15.455][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-01-28 18:26:15.459][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:15.460][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:15.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:15.470][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:15.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:15.472][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:15.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:26:15.475][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2023-01-28 18:26:15.479][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:26:15.480][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:26:15.482][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2023-01-28 18:26:16.565][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2023-01-28 18:26:17.669][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:26:17.679][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2023-01-28 18:26:17.693][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2023-01-28 18:26:17.707][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2023-01-28 18:26:17.728][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-01-28 18:26:17.751][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-01-28 18:26:17.753][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-01-28 18:26:17.755][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:17.756][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:17.757][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:17.766][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:17.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:17.768][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:17.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:26:17.773][ef$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:17.774][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:17.775][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:17.777][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:17.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:17.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:17.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:17.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:17.787][ef$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:26:17.789][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:26:17.790][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:17.792][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:17.794][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:26:17.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:26:17.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:17.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:17.803][ef$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:26:17.805][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:26:17.806][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:17.808][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:17.810][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:26:17.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:26:17.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:17.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:17.820][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:26:17.821][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:26:17.823][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:17.824][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:17.826][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:26:17.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:26:17.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:17.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:17.835][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:26:17.837][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:26:17.838][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:17.840][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:17.841][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:26:17.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:26:17.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:17.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:17.851][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:26:17.853][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:26:17.854][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:17.855][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:17.858][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:26:17.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:26:17.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:17.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:17.867][ef$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:26:17.869][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:17.870][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:17.872][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:17.873][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:26:17.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:17.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:17.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:17.883][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:17.884][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:17.886][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:17.887][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:17.889][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:17.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:17.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:17.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:17.899][ef$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:26:17.900][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:26:17.901][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:17.903][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:17.905][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:26:17.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:26:17.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:17.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:17.914][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:26:17.916][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:26:17.917][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:17.919][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:17.920][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:26:17.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:26:17.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:17.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:17.930][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:26:17.932][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:26:17.933][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:17.934][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:17.936][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:26:17.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:26:17.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:17.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:17.954][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:17.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:17.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:17.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:17.960][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:17.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:17.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:17.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:17.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:17.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:17.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:17.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:17.971][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:17.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:17.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:17.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:17.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:17.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:17.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:17.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:17.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:17.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:17.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:17.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:17.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:17.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:17.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:17.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:17.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:17.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:18.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:18.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:18.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:18.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:18.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:18.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:18.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:18.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:18.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:18.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:18.018][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2023-01-28 18:26:18.020][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:18.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:18.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:18.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:18.025][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:18.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:18.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:18.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:18.031][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:18.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:18.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:18.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:18.037][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:18.038][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:18.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:18.048][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:18.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:18.050][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:18.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:26:18.054][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2023-01-28 18:26:18.055][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-01-28 18:26:18.057][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2023-01-28 18:26:18.059][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-01-28 18:26:18.061][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-01-28 18:26:18.062][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-01-28 18:26:18.064][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-01-28 18:26:18.065][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-01-28 18:26:18.067][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-01-28 18:26:18.072][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:18.073][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:18.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:18.083][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:18.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:18.086][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:18.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:26:18.089][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2023-01-28 18:26:18.093][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:26:18.094][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:26:18.096][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2023-01-28 18:26:19.269][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2023-01-28 18:26:20.597][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:26:20.612][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2023-01-28 18:26:20.644][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2023-01-28 18:26:20.657][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2023-01-28 18:26:20.663][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-01-28 18:26:20.693][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-01-28 18:26:20.695][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-01-28 18:26:20.697][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:20.698][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:20.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:20.707][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:20.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:20.710][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:20.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:26:20.723][ef$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:20.725][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:20.726][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:20.727][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:20.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:20.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:20.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:20.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:20.740][ef$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:26:20.741][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:26:20.743][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:20.744][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:20.746][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:26:20.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:26:20.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:20.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:20.756][ef$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:26:20.757][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:26:20.759][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:20.760][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:20.762][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:26:20.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:26:20.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:20.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:20.771][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:26:20.773][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:26:20.774][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:20.775][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:20.777][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:26:20.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:26:20.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:20.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:20.786][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:26:20.788][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:26:20.789][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:20.790][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:20.792][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:26:20.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:26:20.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:20.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:20.801][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:26:20.802][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:26:20.804][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:20.805][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:20.807][ef$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:26:20.808][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:20.810][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:20.811][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:20.813][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:26:20.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:20.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:20.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:20.822][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:20.824][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:20.825][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:20.826][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:20.828][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:20.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:20.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:20.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:20.837][ef$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:26:20.839][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:26:20.840][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:20.841][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:20.843][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:26:20.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:26:20.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:20.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:20.853][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:26:20.854][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:26:20.856][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:20.857][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:20.859][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:26:20.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:26:20.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:20.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:20.877][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:26:20.878][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:26:20.880][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:20.881][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:20.883][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:26:20.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:26:20.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:20.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:20.892][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:20.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:20.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:20.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:20.898][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:20.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:20.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:20.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:20.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:20.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:20.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:20.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:20.909][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:20.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:20.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:20.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:20.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:20.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:20.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:20.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:20.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:20.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:20.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:20.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:20.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:20.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:20.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:20.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:20.935][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:20.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:20.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:20.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:20.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:20.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:20.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:20.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:20.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:20.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:20.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:20.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:20.952][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2023-01-28 18:26:20.953][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:20.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:20.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:20.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:20.959][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:20.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:20.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:20.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:20.964][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:20.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:20.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:20.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:20.970][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:20.971][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:20.972][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:20.980][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:20.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:20.983][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:20.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:26:20.986][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2023-01-28 18:26:20.987][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-01-28 18:26:20.989][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2023-01-28 18:26:20.991][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-01-28 18:26:20.992][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-01-28 18:26:20.994][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-01-28 18:26:20.995][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-01-28 18:26:20.997][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-01-28 18:26:20.998][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-01-28 18:26:21.003][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:21.004][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:21.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:21.014][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:21.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:21.017][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:21.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:26:21.019][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2023-01-28 18:26:21.023][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:26:21.024][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:26:21.026][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2023-01-28 18:26:22.197][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2023-01-28 18:26:23.712][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:26:23.722][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2023-01-28 18:26:23.736][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2023-01-28 18:26:23.750][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2023-01-28 18:26:23.756][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-01-28 18:26:23.777][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-01-28 18:26:23.779][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-01-28 18:26:23.781][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:23.782][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:23.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:23.791][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:23.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:23.794][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:23.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:26:23.798][ef$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:23.800][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:23.801][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:23.802][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:23.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:23.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:23.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:23.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:23.813][ef$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:26:23.815][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:26:23.816][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:23.817][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:23.819][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:26:23.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:26:23.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:23.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:23.828][ef$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:26:23.830][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:26:23.831][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:23.832][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:23.834][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:26:23.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:26:23.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:23.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:23.843][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:26:23.845][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:26:23.846][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:23.847][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:23.849][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:26:23.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:26:23.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:23.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:23.858][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:26:23.860][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:26:23.861][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:23.863][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:23.864][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:26:23.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:26:23.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:23.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:23.874][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:26:23.876][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:26:23.877][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:23.878][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:23.880][ef$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:26:23.882][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:23.883][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:23.884][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:23.886][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:26:23.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:23.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:23.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:23.895][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:23.897][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:23.898][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:23.900][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:23.901][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:23.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:23.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:23.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:23.911][ef$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:26:23.912][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:26:23.913][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:23.915][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:23.917][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:26:23.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:26:23.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:23.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:23.937][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:26:23.939][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:26:23.940][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:23.941][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:23.943][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:26:23.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:26:23.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:23.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:23.952][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:26:23.954][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:26:23.955][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:23.956][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:23.958][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:26:23.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:26:23.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:23.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:23.967][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:23.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:23.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:23.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:23.973][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:23.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:23.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:23.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:23.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:23.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:23.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:23.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:23.984][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:23.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:23.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:23.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:23.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:23.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:23.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:23.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:23.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:23.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:23.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:23.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:24.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:24.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:24.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:24.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:24.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:24.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:24.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:24.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:24.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:24.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:24.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:24.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:24.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:24.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:24.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:24.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:24.027][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2023-01-28 18:26:24.028][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:24.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:24.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:24.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:24.034][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:24.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:24.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:24.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:24.039][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:24.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:24.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:24.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:24.045][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:24.046][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:24.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:24.055][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:24.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:24.057][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:24.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:26:24.060][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2023-01-28 18:26:24.062][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-01-28 18:26:24.064][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2023-01-28 18:26:24.066][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-01-28 18:26:24.067][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-01-28 18:26:24.069][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-01-28 18:26:24.070][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-01-28 18:26:24.071][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-01-28 18:26:24.073][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-01-28 18:26:24.076][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:24.078][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:24.079][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:24.087][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:24.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:24.089][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:24.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:26:24.092][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2023-01-28 18:26:24.096][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:26:24.097][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:26:24.099][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2023-01-28 18:26:25.226][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2023-01-28 18:26:26.340][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:26:26.349][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2023-01-28 18:26:26.363][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2023-01-28 18:26:26.376][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2023-01-28 18:26:26.381][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-01-28 18:26:26.403][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-01-28 18:26:26.405][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-01-28 18:26:26.407][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:26.408][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:26.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:26.417][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:26.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:26.419][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:26.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:26:26.424][ef$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:26.425][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:26.426][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:26.427][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:26.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:26.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:26.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:26.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:26.438][ef$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:26:26.440][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:26:26.452][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:26.453][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:26.455][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:26:26.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:26:26.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:26.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:26.464][ef$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:26:26.465][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:26:26.467][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:26.468][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:26.470][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:26:26.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:26:26.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:26.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:26.479][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:26:26.480][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:26:26.482][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:26.483][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:26.485][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:26:26.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:26:26.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:26.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:26.494][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:26:26.495][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:26:26.497][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:26.498][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:26.500][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:26:26.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:26:26.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:26.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:26.509][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:26:26.510][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:26:26.512][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:26.513][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:26.515][ef$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:26:26.516][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:26.518][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:26.519][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:26.521][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:26:26.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:26.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:26.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:26.530][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:26.531][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:26.533][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:26.545][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:26.547][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:26.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:26.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:26.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:26.557][ef$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:26:26.558][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:26:26.560][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:26.561][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:26.563][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:26:26.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:26:26.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:26.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:26.572][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:26:26.574][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:26:26.575][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:26.576][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:26.578][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:26:26.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:26:26.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:26.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:26.587][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:26:26.589][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:26:26.590][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:26.592][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:26.593][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:26:26.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:26:26.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:26.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:26.603][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:26.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:26.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:26.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:26.609][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:26.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:26.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:26.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:26.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:26.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:26.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:26.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:26.620][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:26.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:26.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:26.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:26.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:26.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:26.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:26.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:26.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:26.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:26.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:26.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:26.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:26.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:26.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:26.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:26.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:26.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:26.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:26.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:26.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:26.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:26.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:26.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:26.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:26.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:26.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:26.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:26.662][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2023-01-28 18:26:26.663][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:26.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:26.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:26.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:26.669][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:26.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:26.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:26.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:26.674][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:26.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:26.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:26.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:26.680][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:26.681][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:26.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:26.690][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:26.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:26.692][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:26.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:26:26.695][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2023-01-28 18:26:26.696][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-01-28 18:26:26.699][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2023-01-28 18:26:26.700][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-01-28 18:26:26.702][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-01-28 18:26:26.703][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-01-28 18:26:26.705][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-01-28 18:26:26.706][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-01-28 18:26:26.707][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-01-28 18:26:26.711][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:26.712][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:26.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:26.721][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:26.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:26.724][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:26.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:26:26.727][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2023-01-28 18:26:26.731][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:26:26.732][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:26:26.734][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2023-01-28 18:26:27.837][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2023-01-28 18:26:28.962][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:26:28.971][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2023-01-28 18:26:28.986][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2023-01-28 18:26:29.000][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2023-01-28 18:26:29.005][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-01-28 18:26:29.027][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-01-28 18:26:29.029][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-01-28 18:26:29.031][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:29.032][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:29.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:29.042][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:29.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:29.044][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:29.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:26:29.049][ef$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:29.051][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:29.052][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:29.053][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:29.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:29.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:29.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:29.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:29.065][ef$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:26:29.066][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:26:29.067][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:29.069][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:29.070][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:26:29.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:26:29.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:29.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:29.080][ef$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:26:29.082][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:26:29.083][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:29.084][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:29.086][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:26:29.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:26:29.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:29.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:29.095][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:26:29.097][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:26:29.098][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:29.100][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:29.101][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:26:29.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:26:29.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:29.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:29.111][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:26:29.113][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:26:29.114][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:29.116][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:29.117][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:26:29.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:26:29.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:29.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:29.127][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:26:29.128][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:26:29.130][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:29.131][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:29.144][ef$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:26:29.146][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:29.147][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:29.149][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:29.151][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:26:29.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:29.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:29.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:29.160][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:29.162][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:29.163][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:29.165][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:29.166][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:29.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:29.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:29.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:29.176][ef$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:26:29.178][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:26:29.179][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:29.180][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:29.183][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:26:29.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:26:29.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:29.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:29.192][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:26:29.194][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:26:29.196][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:29.197][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:29.199][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:26:29.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:26:29.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:29.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:29.209][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:26:29.210][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:26:29.212][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:29.213][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:29.215][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:26:29.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:26:29.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:29.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:29.224][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:29.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:29.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:29.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:29.230][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:29.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:29.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:29.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:29.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:29.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:29.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:29.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:29.241][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:29.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:29.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:29.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:29.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:29.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:29.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:29.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:29.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:29.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:29.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:29.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:29.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:29.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:29.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:29.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:29.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:29.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:29.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:29.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:29.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:29.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:29.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:29.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:29.279][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:29.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:29.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:29.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:29.284][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2023-01-28 18:26:29.286][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:29.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:29.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:29.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:29.291][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:29.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:29.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:29.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:29.297][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:29.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:29.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:29.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:29.303][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:29.304][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:29.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:29.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:29.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:29.324][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:29.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:26:29.327][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2023-01-28 18:26:29.328][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-01-28 18:26:29.331][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2023-01-28 18:26:29.332][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-01-28 18:26:29.334][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-01-28 18:26:29.335][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-01-28 18:26:29.337][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-01-28 18:26:29.338][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-01-28 18:26:29.340][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-01-28 18:26:29.343][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:29.344][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:29.346][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:29.354][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:29.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:29.356][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:29.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:26:29.359][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2023-01-28 18:26:29.363][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:26:29.364][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:26:29.375][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2023-01-28 18:26:30.586][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2023-01-28 18:26:31.723][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:26:31.732][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2023-01-28 18:26:31.746][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2023-01-28 18:26:31.760][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2023-01-28 18:26:31.765][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-01-28 18:26:31.787][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-01-28 18:26:31.789][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-01-28 18:26:31.791][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:31.793][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:31.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:31.802][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:31.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:31.805][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:31.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:26:31.809][ef$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:31.811][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:31.812][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:31.813][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:31.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:31.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:31.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:31.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:31.824][ef$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:26:31.826][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:26:31.827][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:31.829][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:31.830][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:26:31.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:26:31.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:31.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:31.840][ef$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:26:31.841][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:26:31.843][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:31.845][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:31.848][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:26:31.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:26:31.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:31.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:31.858][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:26:31.860][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:26:31.861][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:31.862][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:31.864][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:26:31.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:26:31.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:31.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:31.888][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:26:31.890][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:26:31.891][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:31.892][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:31.894][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:26:31.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:26:31.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:31.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:31.903][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:26:31.905][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:26:31.906][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:31.908][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:31.910][ef$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:26:31.911][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:31.913][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:31.914][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:31.916][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:26:31.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:31.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:31.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:31.925][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:31.926][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:31.928][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:31.929][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:31.931][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:31.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:31.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:31.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:31.940][ef$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:26:31.942][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:26:31.943][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:31.945][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:31.947][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:26:31.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:26:31.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:31.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:31.956][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:26:31.958][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:26:31.959][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:31.960][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:31.962][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:26:31.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:26:31.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:31.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:31.971][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:26:31.973][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:26:31.974][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:31.976][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:31.977][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:26:31.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:26:31.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:31.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:31.987][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:31.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:31.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:31.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:31.993][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:31.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:31.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:31.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:31.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:32.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:32.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:32.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:32.004][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:32.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:32.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:32.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:32.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:32.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:32.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:32.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:32.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:32.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:32.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:32.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:32.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:32.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:32.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:32.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:32.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:32.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:32.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:32.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:32.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:32.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:32.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:32.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:32.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:32.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:32.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:32.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:32.048][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2023-01-28 18:26:32.049][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:32.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:32.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:32.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:32.055][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:32.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:32.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:32.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:32.061][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:32.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:32.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:32.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:32.066][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:32.067][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:32.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:32.077][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:32.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:32.079][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:32.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:26:32.082][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2023-01-28 18:26:32.083][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-01-28 18:26:32.085][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2023-01-28 18:26:32.087][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-01-28 18:26:32.089][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-01-28 18:26:32.090][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-01-28 18:26:32.092][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-01-28 18:26:32.093][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-01-28 18:26:32.094][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-01-28 18:26:32.106][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:32.108][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:32.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:32.118][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:32.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:32.120][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:32.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:26:32.123][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2023-01-28 18:26:32.127][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:26:32.128][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:26:32.130][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2023-01-28 18:26:33.260][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2023-01-28 18:26:35.841][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:26:35.852][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2023-01-28 18:26:35.867][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2023-01-28 18:26:35.882][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2023-01-28 18:26:35.887][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-01-28 18:26:35.911][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-01-28 18:26:35.912][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-01-28 18:26:35.915][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:35.916][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:35.917][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:35.925][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:35.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:35.928][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:35.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:26:35.932][ef$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:35.933][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:35.935][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:35.936][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:35.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:35.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:35.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:35.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:35.947][ef$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:26:35.948][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:26:35.949][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:35.951][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:35.952][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:26:35.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:26:35.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:35.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:35.962][ef$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:26:35.963][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:26:35.965][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:35.966][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:35.968][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:26:35.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:26:35.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:35.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:35.992][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:26:35.994][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:26:35.995][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:35.996][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:35.998][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:26:35.999][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:26:36.001][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:36.002][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:36.004][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:26:36.005][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:26:36.006][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:36.008][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:36.009][ef$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:26:36.011][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:36.012][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:36.014][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:36.015][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:26:36.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:36.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:36.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:36.025][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:36.027][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:36.029][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:36.030][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:36.032][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:36.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:36.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:36.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:36.042][ef$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:26:36.043][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:26:36.045][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:36.046][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:36.048][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:26:36.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:26:36.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:36.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:36.058][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:26:36.059][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:26:36.061][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:36.062][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:36.064][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:26:36.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:26:36.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:36.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:36.074][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:26:36.075][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:26:36.077][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:36.078][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:36.080][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:36.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:36.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:36.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:36.085][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:36.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:36.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:36.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:36.091][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:36.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:36.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:36.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:36.097][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:36.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:36.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:36.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:36.102][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:36.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:36.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:36.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:36.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:36.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:36.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:36.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:36.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:36.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:36.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:36.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:36.123][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:36.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:36.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:36.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:36.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:36.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:36.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:36.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:36.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:36.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:36.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:36.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:36.140][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2023-01-28 18:26:36.142][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:36.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:36.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:36.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:36.147][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:36.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:36.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:36.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:36.153][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:36.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:36.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:36.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:36.159][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:36.160][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:36.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:36.169][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:36.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:36.172][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:36.173][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[2023-01-28 18:26:36.175][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2023-01-28 18:26:36.176][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-01-28 18:26:36.178][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2023-01-28 18:26:36.180][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-01-28 18:26:36.182][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-01-28 18:26:36.183][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-01-28 18:26:36.184][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-01-28 18:26:36.186][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-01-28 18:26:36.187][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-01-28 18:26:36.191][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:36.192][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:36.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:36.211][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:36.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:36.213][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:36.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:26:36.216][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2023-01-28 18:26:36.220][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:26:36.221][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:26:36.223][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2023-01-28 18:26:37.405][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2023-01-28 18:26:38.621][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:26:38.633][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2023-01-28 18:26:38.647][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2023-01-28 18:26:38.660][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2023-01-28 18:26:38.666][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-01-28 18:26:38.687][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-01-28 18:26:38.689][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-01-28 18:26:38.691][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:38.693][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:38.694][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:38.702][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:38.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:38.705][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:38.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:26:38.709][ef$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:38.710][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:38.712][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:38.713][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:38.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:38.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:38.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:38.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:38.724][ef$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:26:38.725][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:26:38.727][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:38.728][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:38.730][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:26:38.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:26:38.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:38.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:38.739][ef$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:26:38.740][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:26:38.742][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:38.743][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:38.745][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:26:38.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:26:38.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:38.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:38.768][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:26:38.770][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:26:38.771][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:38.773][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:38.774][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:26:38.776][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:26:38.777][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:38.778][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:38.780][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:26:38.781][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:26:38.783][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:38.784][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:38.785][ef$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:26:38.787][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:38.788][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:38.790][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:38.791][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:26:38.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:38.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:38.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:38.800][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:38.802][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:38.803][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:38.805][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:38.806][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:38.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:38.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:38.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:38.816][ef$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:26:38.817][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:26:38.819][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:38.820][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:38.822][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:26:38.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:26:38.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:38.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:38.831][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:26:38.833][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:26:38.834][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:38.836][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:38.837][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:26:38.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:26:38.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:38.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:38.847][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:26:38.848][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:26:38.850][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:38.851][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:38.853][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:38.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:38.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:38.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:38.859][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:38.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:38.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:38.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:38.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:38.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:38.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:38.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:38.870][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:38.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:38.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:38.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:38.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:38.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:38.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:38.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:38.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:38.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:38.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:38.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:38.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:38.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:38.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:38.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:38.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:38.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:38.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:38.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:38.902][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:38.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:38.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:38.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:38.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:38.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:38.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:38.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:38.914][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2023-01-28 18:26:38.915][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:38.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:38.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:38.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:38.921][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:38.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:38.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:38.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:38.927][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:38.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:38.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:38.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:38.932][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:38.934][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:38.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:38.943][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:38.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:38.946][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:38.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:26:38.948][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2023-01-28 18:26:38.950][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-01-28 18:26:38.952][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2023-01-28 18:26:38.954][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-01-28 18:26:38.956][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-01-28 18:26:38.957][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-01-28 18:26:38.959][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-01-28 18:26:38.960][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-01-28 18:26:38.961][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-01-28 18:26:38.965][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:38.967][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:38.968][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:38.985][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:38.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:38.989][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:38.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:26:38.992][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2023-01-28 18:26:38.996][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:26:38.997][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:26:38.999][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2023-01-28 18:26:40.304][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2023-01-28 18:26:41.406][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:26:41.416][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2023-01-28 18:26:41.432][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2023-01-28 18:26:41.447][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2023-01-28 18:26:41.452][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-01-28 18:26:41.475][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-01-28 18:26:41.477][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-01-28 18:26:41.479][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:41.480][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:41.482][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:41.490][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:41.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:41.493][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:41.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:26:41.498][ef$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:41.499][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:41.501][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:41.502][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:41.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:41.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:41.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:41.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:41.514][ef$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:26:41.515][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:26:41.517][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:41.518][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:41.520][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:26:41.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:26:41.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:41.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:41.531][ef$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:26:41.532][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:26:41.534][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:41.536][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:41.537][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:26:41.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:26:41.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:41.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:41.753][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:26:41.755][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:26:41.756][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:41.757][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:41.759][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:26:41.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:26:41.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:41.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:41.768][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:26:41.770][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:26:41.771][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:41.772][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:41.774][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:26:41.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:26:41.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:41.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:41.783][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:26:41.785][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:26:41.786][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:41.787][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:41.789][ef$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:26:41.791][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:41.792][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:41.793][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:41.795][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:26:41.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:41.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:41.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:41.804][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:41.806][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:41.807][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:41.808][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:41.810][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:41.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:41.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:41.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:41.820][ef$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:26:41.821][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:26:41.823][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:41.824][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:41.826][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:26:41.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:26:41.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:41.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:41.836][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:26:41.837][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:26:41.839][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:41.840][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:41.842][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:26:41.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:26:41.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:41.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:41.851][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:26:41.853][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:26:41.854][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:41.855][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:41.857][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:26:41.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:26:41.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:41.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:41.867][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:41.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:41.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:41.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:41.873][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:41.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:41.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:41.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:41.878][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:41.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:41.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:41.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:41.884][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:41.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:41.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:41.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:41.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:41.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:41.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:41.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:41.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:41.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:41.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:41.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:41.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:41.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:41.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:41.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:41.911][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:41.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:41.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:41.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:41.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:41.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:41.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:41.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:41.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:41.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:41.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:41.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:41.927][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2023-01-28 18:26:41.929][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:41.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:41.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:41.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:41.935][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:41.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:41.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:41.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:41.940][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:41.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:41.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:41.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:41.946][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:41.947][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:41.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:41.956][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:41.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:41.959][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:41.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:26:41.961][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2023-01-28 18:26:41.963][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-01-28 18:26:41.965][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2023-01-28 18:26:41.967][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-01-28 18:26:41.968][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-01-28 18:26:41.969][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-01-28 18:26:41.971][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-01-28 18:26:41.972][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-01-28 18:26:41.974][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-01-28 18:26:41.977][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:41.978][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:41.979][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:41.987][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:41.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:41.990][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:41.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:26:41.993][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2023-01-28 18:26:41.996][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:26:41.998][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:26:41.999][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2023-01-28 18:26:43.108][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2023-01-28 18:26:44.258][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:26:44.269][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2023-01-28 18:26:44.286][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2023-01-28 18:26:44.302][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2023-01-28 18:26:44.308][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-01-28 18:26:44.333][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-01-28 18:26:44.335][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-01-28 18:26:44.338][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:44.339][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:44.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:44.349][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:44.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:44.352][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:44.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:26:44.357][ef$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:44.359][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:44.361][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:44.362][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:44.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:44.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:44.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:44.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:44.375][ef$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:26:44.376][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:26:44.378][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:44.380][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:44.382][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:26:44.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:26:44.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:44.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:44.392][ef$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:26:44.394][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:26:44.396][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:44.397][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:44.399][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:26:44.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:26:44.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:44.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:44.423][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:26:44.425][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:26:44.426][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:44.427][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:44.429][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:26:44.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:26:44.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:44.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:44.438][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:26:44.439][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:26:44.441][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:44.442][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:44.444][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:26:44.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:26:44.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:44.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:44.453][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:26:44.454][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:26:44.456][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:44.457][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:44.458][ef$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:26:44.460][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:44.461][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:44.463][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:44.464][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:26:44.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:44.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:44.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:44.473][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:44.475][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:44.476][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:44.477][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:44.479][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:44.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:44.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:44.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:44.488][ef$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:26:44.490][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:26:44.491][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:44.492][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:44.494][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:26:44.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:26:44.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:44.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:44.503][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:26:44.505][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:26:44.506][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:44.508][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:44.509][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:26:44.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:26:44.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:44.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:44.518][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:26:44.520][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:26:44.521][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:44.522][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:44.524][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:26:44.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:26:44.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:44.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:44.542][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:44.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:44.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:44.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:44.548][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:44.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:44.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:44.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:44.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:44.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:44.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:44.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:44.559][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:44.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:44.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:44.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:44.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:44.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:44.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:44.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:44.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:44.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:44.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:44.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:44.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:44.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:44.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:44.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:44.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:44.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:44.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:44.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:44.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:44.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:44.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:44.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:44.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:44.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:44.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:44.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:44.601][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2023-01-28 18:26:44.603][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:44.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:44.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:44.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:44.608][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:44.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:44.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:44.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:44.614][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:44.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:44.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:44.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:44.620][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:44.621][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:44.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:44.631][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:44.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:44.634][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:44.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:26:44.636][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2023-01-28 18:26:44.638][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-01-28 18:26:44.640][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2023-01-28 18:26:44.642][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-01-28 18:26:44.643][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-01-28 18:26:44.645][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-01-28 18:26:44.646][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-01-28 18:26:44.647][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-01-28 18:26:44.649][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-01-28 18:26:44.652][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:44.653][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:44.655][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:44.663][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:44.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:44.665][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:44.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:26:44.668][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2023-01-28 18:26:44.672][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:26:44.673][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:26:44.675][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2023-01-28 18:26:45.784][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2023-01-28 18:26:46.894][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:26:46.903][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2023-01-28 18:26:46.918][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2023-01-28 18:26:46.933][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2023-01-28 18:26:46.938][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-01-28 18:26:46.976][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-01-28 18:26:46.978][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-01-28 18:26:46.981][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:46.982][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:46.983][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:46.997][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:46.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:46.999][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:47.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:26:47.004][ef$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:47.005][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:47.007][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:47.008][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:47.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:47.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:47.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:47.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:47.034][ef$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:26:47.036][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:26:47.037][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:47.039][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:47.041][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:26:47.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:26:47.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:47.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:47.052][ef$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:26:47.053][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:26:47.055][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:47.057][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:47.059][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:26:47.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:26:47.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:47.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:47.085][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:26:47.087][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:26:47.089][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:47.090][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:47.093][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:26:47.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:26:47.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:47.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:47.103][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:26:47.105][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:26:47.106][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:47.108][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:47.110][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:26:47.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:26:47.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:47.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:47.119][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:26:47.121][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:26:47.122][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:47.124][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:47.125][ef$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:26:47.127][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:47.128][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:47.130][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:47.131][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:26:47.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:47.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:47.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:47.141][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:47.142][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:47.144][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:47.145][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:47.147][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:47.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:47.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:47.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:47.156][ef$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:26:47.158][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:26:47.159][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:47.161][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:47.163][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:26:47.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:26:47.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:47.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:47.172][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:26:47.173][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:26:47.175][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:47.176][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:47.178][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:26:47.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:26:47.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:47.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:47.187][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:26:47.189][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:26:47.190][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:47.192][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:47.193][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:26:47.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:26:47.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:47.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:47.203][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:47.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:47.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:47.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:47.208][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:47.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:47.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:47.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:47.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:47.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:47.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:47.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:47.220][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:47.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:47.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:47.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:47.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:47.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:47.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:47.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:47.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:47.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:47.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:47.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:47.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:47.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:47.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:47.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:47.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:47.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:47.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:47.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:47.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:47.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:47.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:47.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:47.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:47.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:47.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:47.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:47.263][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2023-01-28 18:26:47.264][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:47.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:47.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:47.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:47.270][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:47.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:47.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:47.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:47.275][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:47.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:47.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:47.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:47.281][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:47.282][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:47.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:47.291][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:47.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:47.294][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:47.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:26:47.297][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2023-01-28 18:26:47.298][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-01-28 18:26:47.300][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2023-01-28 18:26:47.302][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-01-28 18:26:47.304][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-01-28 18:26:47.305][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-01-28 18:26:47.307][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-01-28 18:26:47.308][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-01-28 18:26:47.309][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-01-28 18:26:47.313][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:47.314][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:47.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:47.324][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:47.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:47.326][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:47.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:26:47.329][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2023-01-28 18:26:47.333][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:26:47.335][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:26:47.337][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2023-01-28 18:26:48.438][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2023-01-28 18:26:49.565][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:26:49.578][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2023-01-28 18:26:49.593][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2023-01-28 18:26:49.607][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2023-01-28 18:26:49.612][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-01-28 18:26:49.635][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-01-28 18:26:49.636][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-01-28 18:26:49.638][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:49.640][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:49.641][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:49.649][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:49.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:49.652][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:49.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:26:49.656][ef$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:49.657][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:49.659][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:49.660][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:49.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:49.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:49.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:49.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:49.671][ef$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:26:49.673][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:26:49.675][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:49.676][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:49.678][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:26:49.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:26:49.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:49.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:49.687][ef$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:26:49.689][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:26:49.690][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:49.691][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:49.693][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:26:49.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:26:49.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:49.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:49.716][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:26:49.718][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:26:49.719][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:49.721][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:49.722][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:26:49.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:26:49.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:49.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:49.731][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:26:49.733][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:26:49.734][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:49.735][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:49.737][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:26:49.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:26:49.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:49.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:49.746][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:26:49.748][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:26:49.749][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:49.750][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:49.752][ef$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:26:49.753][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:49.755][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:49.756][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:49.758][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:26:49.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:49.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:49.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:49.768][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:49.770][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:49.771][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:49.773][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:49.774][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:49.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:49.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:49.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:49.784][ef$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:26:49.786][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:26:49.787][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:49.788][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:49.790][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:26:49.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:26:49.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:49.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:49.800][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:26:49.802][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:26:49.803][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:49.804][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:49.806][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:26:49.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:26:49.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:49.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:49.816][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:26:49.817][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:26:49.819][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:49.820][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:49.822][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:26:49.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:26:49.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:49.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:49.831][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:49.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:49.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:49.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:49.837][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:49.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:49.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:49.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:49.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:49.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:49.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:49.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:49.848][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:49.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:49.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:49.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:49.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:49.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:49.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:49.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:49.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:49.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:49.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:49.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:49.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:49.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:49.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:49.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:49.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:49.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:49.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:49.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:49.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:49.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:49.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:49.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:49.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:49.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:49.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:49.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:49.892][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2023-01-28 18:26:49.894][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:49.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:49.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:49.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:49.900][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:49.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:49.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:49.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:49.905][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:49.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:49.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:49.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:49.911][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:49.912][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:49.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:49.922][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:49.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:49.925][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:49.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:26:49.927][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2023-01-28 18:26:49.929][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-01-28 18:26:49.931][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2023-01-28 18:26:49.933][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-01-28 18:26:49.935][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-01-28 18:26:49.936][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-01-28 18:26:49.938][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-01-28 18:26:49.939][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-01-28 18:26:49.940][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-01-28 18:26:49.944][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:49.945][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:49.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:49.955][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:49.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:49.958][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:49.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:26:49.961][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2023-01-28 18:26:49.965][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:26:49.966][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:26:49.968][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2023-01-28 18:26:51.060][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2023-01-28 18:26:52.154][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:26:52.165][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2023-01-28 18:26:52.182][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2023-01-28 18:26:52.197][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2023-01-28 18:26:52.203][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-01-28 18:26:52.227][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-01-28 18:26:52.229][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-01-28 18:26:52.231][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:52.233][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:52.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:52.243][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:52.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:52.246][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:52.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:26:52.250][ef$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:52.252][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:52.253][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.255][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:52.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:52.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.267][ef$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:26:52.268][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:26:52.270][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.271][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.273][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:26:52.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:26:52.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.284][ef$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:26:52.285][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:26:52.287][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.288][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.290][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:26:52.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:26:52.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.316][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:26:52.317][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:26:52.319][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.321][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.323][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:26:52.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:26:52.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.332][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:26:52.334][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:26:52.335][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.337][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.339][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:26:52.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:26:52.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.348][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:26:52.350][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:26:52.351][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.353][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.355][ef$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:26:52.356][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.358][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.359][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.361][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:26:52.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.371][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:52.372][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:52.374][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.375][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.377][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:52.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:52.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.386][ef$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:26:52.388][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:26:52.389][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.391][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.393][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:26:52.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:26:52.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.402][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:26:52.404][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:26:52.405][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.407][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.409][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:26:52.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:26:52.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.418][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:26:52.420][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:26:52.421][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.423][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.425][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:26:52.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:26:52.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.434][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:52.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:52.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.440][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:52.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:52.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:52.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:52.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.452][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:26:52.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:26:52.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.458][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:52.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:52.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.464][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:52.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:52.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:52.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:52.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.480][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:52.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:52.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:52.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:52.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.492][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:26:52.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:26:52.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:52.498][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2023-01-28 18:26:52.500][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.506][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.512][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:52.571][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:26:52.576][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-01-28 18:26:52.578][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-01-28 18:26:52.580][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-01-28 18:26:52.583][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-01-28 18:26:52.610][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:52.612][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:52.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:52.623][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:52.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:52.626][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:52.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:26:52.629][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.635][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.640][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:52.646][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:52.648][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:52.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:52.657][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:52.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:52.660][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:52.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:26:52.663][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.669][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.675][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.681][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.687][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:52.693][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:52.694][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:52.695][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:52.704][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:52.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:52.707][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:52.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:26:52.711][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.717][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.724][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.730][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.737][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:52.743][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:52.744][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:52.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:52.754][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:52.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:52.756][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:52.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:26:52.759][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.765][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.771][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.777][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.792][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:52.798][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:52.799][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:52.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:52.809][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:52.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:52.812][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:52.813][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[2023-01-28 18:26:52.815][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.821][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.827][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:52.833][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:52.834][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:52.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:52.844][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:52.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:52.847][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:52.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:26:52.850][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.856][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.861][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:52.867][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:52.868][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:52.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:52.878][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:52.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:52.881][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:52.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:26:52.884][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.889][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.895][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:52.901][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:52.902][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:52.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:52.912][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:52.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:52.915][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:52.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:26:52.918][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.924][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.930][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:52.936][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:52.937][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:52.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:52.947][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:52.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:52.951][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:52.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:26:52.954][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.960][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.966][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:52.973][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:52.974][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:52.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:52.984][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:52.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:52.987][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:52.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:26:52.990][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:52.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:52.996][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:52.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:53.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:53.001][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:53.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:53.007][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:53.008][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:53.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:53.018][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:53.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:53.020][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:53.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:26:53.023][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:53.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:53.029][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:53.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:53.035][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:53.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:53.040][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:53.041][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:53.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:53.051][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:53.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:53.053][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:53.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:26:53.056][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:53.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:53.062][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:53.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:53.068][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:53.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:53.074][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:53.075][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:53.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:53.085][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:53.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:53.088][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:53.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:26:53.091][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:53.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:53.096][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:53.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:53.102][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:53.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:53.108][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:53.109][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:53.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:53.119][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:53.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:53.122][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:53.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:26:53.125][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:53.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:53.130][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:53.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:53.136][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:53.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:53.142][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:53.143][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:53.144][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:53.153][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:53.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:53.156][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:53.157][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.TRACE[2023-01-28 18:26:53.159][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:53.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:53.165][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:53.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:53.171][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:53.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:53.176][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:53.178][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:53.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:53.187][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:53.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:53.190][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:53.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:26:53.192][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:53.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:53.198][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:53.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:53.203][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:53.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:53.209][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:53.210][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:53.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:53.219][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:53.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:53.222][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:53.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:26:53.225][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:53.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:53.230][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:53.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:53.236][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:53.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:53.249][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:53.251][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:53.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:53.261][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:53.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:53.263][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:53.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:26:53.267][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:53.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:53.273][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:53.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:53.279][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:26:53.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:53.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:53.311][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:53.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:53.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:53.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:53.317][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:53.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:53.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:53.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:53.323][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:53.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:53.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:53.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:53.328][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:53.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:53.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:53.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:26:53.334][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:53.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:26:53.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:26:53.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:26:53.416][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:26:53.421][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:26:53.422][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:26:53.425][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-01-28 18:26:54.603][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-01-28 18:26:55.768][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:26:55.778][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2023-01-28 18:26:55.794][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2023-01-28 18:26:55.802][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:26:55.806][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:26:55.808][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:26:55.810][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-01-28 18:26:56.904][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-01-28 18:26:58.034][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:26:58.043][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2023-01-28 18:26:58.059][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2023-01-28 18:26:58.066][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:58.067][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:58.068][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:58.077][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:58.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:58.080][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:58.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:26:58.083][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2023-01-28 18:26:58.085][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-01-28 18:26:58.087][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2023-01-28 18:26:58.089][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-01-28 18:26:58.090][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-01-28 18:26:58.092][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-01-28 18:26:58.094][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-01-28 18:26:58.095][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-01-28 18:26:58.097][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-01-28 18:26:58.100][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:26:58.102][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:26:58.103][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:26:58.112][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:26:58.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:26:58.115][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:26:58.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:26:58.118][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2023-01-28 18:26:58.122][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:26:58.124][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:26:58.126][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2023-01-28 18:26:59.284][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2023-01-28 18:27:00.468][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:27:00.477][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2023-01-28 18:27:00.492][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2023-01-28 18:27:00.506][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2023-01-28 18:27:00.512][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-01-28 18:27:00.534][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-01-28 18:27:00.535][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-01-28 18:27:00.538][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:00.539][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:00.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:00.550][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:00.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:00.552][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:00.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:00.556][ef$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:00.558][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:00.559][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:00.560][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:00.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:00.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:00.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:00.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:00.571][ef$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:27:00.573][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:27:00.574][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:00.575][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:00.577][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:27:00.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:27:00.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:00.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:00.586][ef$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:27:00.588][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:27:00.589][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:00.590][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:00.592][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:27:00.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:27:00.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:00.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:00.602][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:27:00.603][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:27:00.604][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:00.606][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:00.607][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:27:00.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:27:00.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:00.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:00.617][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:27:00.618][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:27:00.620][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:00.621][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:00.623][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:27:00.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:27:00.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:00.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:00.632][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:27:00.633][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:27:00.635][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:00.636][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:00.638][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:27:00.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:27:00.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:00.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:00.647][ef$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:27:00.648][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:00.650][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:00.651][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:00.653][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:27:00.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:00.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:00.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:00.662][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:00.663][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:00.665][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:00.666][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:00.668][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:00.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:00.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:00.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:00.677][ef$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:27:00.679][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:27:00.680][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:00.681][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:00.683][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:27:00.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:27:00.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:00.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:00.693][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:27:00.694][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:27:00.696][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:00.697][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:00.699][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:27:00.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:27:00.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:00.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:00.708][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:27:00.709][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:27:00.711][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:00.712][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:00.714][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:27:00.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:27:00.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:00.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:00.723][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:00.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:00.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:00.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:00.729][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:00.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:00.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:00.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:00.734][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:00.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:00.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:00.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:00.740][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:00.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:00.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:00.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:00.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:00.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:00.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:00.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:00.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:00.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:00.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:00.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:00.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:00.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:00.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:00.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:00.766][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:00.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:00.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:00.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:00.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:00.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:00.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:00.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:00.777][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:00.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:00.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:00.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:00.783][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2023-01-28 18:27:00.784][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:00.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:00.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:00.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:00.790][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:00.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:00.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:00.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:00.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:00.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:00.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:00.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:00.801][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:00.802][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:00.803][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:00.811][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:00.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:00.814][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:00.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:00.816][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:00.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:00.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:00.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:00.822][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:00.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:00.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:00.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:00.827][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:00.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:00.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:00.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:00.833][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:00.834][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:00.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:00.843][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:00.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:00.846][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:00.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:00.848][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2023-01-28 18:27:00.864][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-01-28 18:27:00.866][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2023-01-28 18:27:00.867][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-01-28 18:27:00.869][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-01-28 18:27:00.870][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-01-28 18:27:00.872][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-01-28 18:27:00.873][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-01-28 18:27:00.874][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-01-28 18:27:00.878][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:00.879][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:00.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:00.889][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:00.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:00.891][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:00.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:00.894][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2023-01-28 18:27:00.898][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:27:00.899][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:27:00.901][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2023-01-28 18:27:01.980][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2023-01-28 18:27:03.888][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:27:03.898][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2023-01-28 18:27:03.912][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2023-01-28 18:27:03.927][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2023-01-28 18:27:03.933][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-01-28 18:27:03.955][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-01-28 18:27:03.957][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-01-28 18:27:03.959][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:03.960][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:03.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:03.970][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:03.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:03.973][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:03.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:03.977][ef$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:03.978][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:03.980][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:03.981][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:03.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:03.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:03.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:03.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:03.992][ef$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:27:03.993][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:27:03.995][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:03.996][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:03.998][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:27:03.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:27:04.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.007][ef$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:27:04.008][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:27:04.010][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.011][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.013][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:27:04.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:27:04.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.022][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:27:04.023][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:27:04.025][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.026][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.028][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:27:04.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:27:04.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.037][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:27:04.038][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:27:04.040][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.041][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.043][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:27:04.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:27:04.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.052][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:27:04.053][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:27:04.055][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.056][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.058][ef$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:27:04.059][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:04.061][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.062][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.064][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:27:04.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:04.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.073][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.075][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.076][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.078][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.079][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.089][ef$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:27:04.090][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:27:04.092][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.093][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.095][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:27:04.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:27:04.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.104][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:27:04.106][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:27:04.107][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.108][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.110][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:27:04.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:27:04.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.120][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:27:04.121][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:27:04.122][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.124][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.125][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:27:04.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:27:04.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.135][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:04.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:04.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.140][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:04.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:04.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:04.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:04.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.152][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:04.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:04.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:04.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:04.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:04.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:04.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:04.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:04.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:04.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:04.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:04.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:04.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:04.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:04.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:04.195][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2023-01-28 18:27:04.196][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.202][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.207][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:04.283][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:27:04.288][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-01-28 18:27:04.290][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-01-28 18:27:04.291][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-01-28 18:27:04.293][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-01-28 18:27:04.316][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:04.317][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:04.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:04.328][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:04.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:04.331][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:04.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:04.333][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.339][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.344][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:04.350][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:04.351][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:04.352][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:04.360][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:04.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:04.363][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:04.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:04.366][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.371][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.377][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.382][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.388][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:04.393][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:04.394][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:04.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:04.404][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:04.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:04.406][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:04.407][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.TRACE[2023-01-28 18:27:04.409][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.414][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.420][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.426][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.431][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:04.437][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:04.438][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:04.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:04.447][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:04.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:04.449][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:04.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:04.452][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.458][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.463][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.469][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.474][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:04.480][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:04.481][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:04.482][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:04.490][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:04.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:04.493][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:04.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:04.496][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.501][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.506][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:04.512][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:04.513][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:04.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:04.522][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:04.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:04.525][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:04.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:04.528][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.533][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.539][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:04.544][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:04.545][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:04.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:04.554][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:04.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:04.557][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:04.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:04.560][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.566][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.571][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:04.577][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:04.578][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:04.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:04.587][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:04.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:04.590][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:04.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:04.593][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.598][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.603][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:04.608][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:04.610][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:04.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:04.619][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:04.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:04.622][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:04.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:04.625][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.631][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.636][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:04.642][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:04.643][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:04.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:04.652][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:04.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:04.655][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:04.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:04.657][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.663][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.676][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:04.682][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:04.683][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:04.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:04.692][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:04.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:04.694][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:04.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:04.697][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.702][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.708][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:04.713][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:04.715][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:04.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:04.724][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:04.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:04.726][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:04.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:04.729][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.734][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.740][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:04.746][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:04.747][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:04.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:04.756][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:04.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:04.758][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:04.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:04.761][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.767][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.772][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:04.777][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:04.779][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:04.780][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:04.788][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:04.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:04.790][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:04.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:04.793][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.798][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.804][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:04.809][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:04.810][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:04.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:04.819][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:04.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:04.822][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:04.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:04.825][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.830][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.835][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:04.841][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:04.842][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:04.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:04.851][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:04.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:04.853][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:04.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:04.856][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.862][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.867][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:04.873][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:04.874][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:04.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:04.883][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:04.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:04.885][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:04.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:04.888][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.894][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.899][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:04.904][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:04.906][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:04.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:04.915][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:04.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:04.917][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:04.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:04.920][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.926][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:04.931][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:04.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:04.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:04.997][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:27:05.001][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-01-28 18:27:05.003][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-01-28 18:27:05.005][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-01-28 18:27:05.006][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-01-28 18:27:05.046][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:05.048][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:05.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:05.057][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:05.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:05.059][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:05.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:05.062][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.067][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.073][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:05.078][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:05.080][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:05.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:05.089][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:05.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:05.091][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:05.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:05.094][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.099][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.105][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.110][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.116][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:05.121][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:05.122][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:05.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:05.139][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:05.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:05.142][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:05.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:05.145][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.150][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.156][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.161][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.166][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:05.172][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:05.173][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:05.174][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:05.182][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:05.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:05.185][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:05.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:05.188][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.193][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.199][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.204][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.210][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:05.215][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:05.216][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:05.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:05.225][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:05.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:05.228][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:05.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:05.231][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.236][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.241][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:05.246][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:05.248][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:05.249][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:05.256][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:05.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:05.259][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:05.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:05.262][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.267][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.272][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:05.278][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:05.279][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:05.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:05.288][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:05.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:05.291][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:05.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:05.294][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.299][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.305][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:05.310][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:05.311][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:05.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:05.320][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:05.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:05.323][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:05.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:05.326][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.331][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.337][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:05.342][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:05.343][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:05.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:05.352][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:05.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:05.355][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:05.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:05.358][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.363][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.369][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:05.375][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:05.376][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:05.377][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:05.385][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:05.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:05.387][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:05.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:05.390][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.396][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.401][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:05.407][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:05.408][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:05.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:05.417][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:05.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:05.419][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:05.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:05.422][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.428][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.433][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:05.438][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:05.439][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:05.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:05.448][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:05.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:05.451][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:05.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:05.454][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.459][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.465][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:05.470][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:05.471][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:05.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:05.480][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:05.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:05.483][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:05.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:05.486][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.491][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.496][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:05.502][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:05.503][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:05.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:05.512][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:05.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:05.515][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:05.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:05.518][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.523][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.528][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:05.533][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:05.535][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:05.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:05.544][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:05.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:05.546][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:05.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:05.556][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.562][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.567][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:05.572][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:05.574][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:05.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:05.582][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:05.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:05.585][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:05.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:05.588][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.593][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.599][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:05.604][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:05.605][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:05.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:05.614][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:05.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:05.617][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:05.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:05.619][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.625][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.630][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:05.635][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:05.637][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:05.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:05.646][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:05.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:05.648][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:05.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:05.651][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.656][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.661][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:05.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.691][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-01-28 18:27:05.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-01-28 18:27:05.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-01-28 18:27:05.712][biodb::testThat]
biodb.INFO [2023-01-28 18:27:05.714][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2023-01-28 18:27:05.715][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-01-28 18:27:05.716][biodb::testThat]
biodb.TRACE[2023-01-28 18:27:05.721][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-01-28 18:27:05.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-01-28 18:27:05.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.727][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:05.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:05.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.733][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:05.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:05.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.738][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:05.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:05.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:05.744][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:05.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:05.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:05.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:05.760][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:05.761][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:05.762][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:05.770][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:05.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:05.773][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:05.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:05.828][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:27:05.832][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:27:05.834][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:27:05.836][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-01-28 18:27:06.925][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-01-28 18:27:08.049][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:27:08.058][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2023-01-28 18:27:08.073][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2023-01-28 18:27:08.080][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:08.082][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:08.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:08.091][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:08.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:08.094][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:08.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:08.097][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:08.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:08.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:08.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:08.102][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:08.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:08.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:08.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:08.108][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:08.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:08.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:08.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:08.115][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:27:08.119][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-01-28 18:27:08.121][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2023-01-28 18:27:08.122][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-01-28 18:27:08.125][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2023-01-28 18:27:08.128][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:08.129][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:08.130][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:08.154][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:08.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:08.157][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:08.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:08.159][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:08.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:08.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:08.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:08.165][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:08.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:08.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:08.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:08.172][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:08.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:08.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:08.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:08.178][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:27:08.183][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-01-28 18:27:08.185][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba".
biodb.TRACE[2023-01-28 18:27:08.187][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-01-28 18:27:08.190][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content".
biodb.DEBUG[2023-01-28 18:27:08.193][private$bdb$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-01-28 18:27:08.195][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:08.196][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:08.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:08.205][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:08.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:08.208][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:08.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:08.211][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:08.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:08.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:08.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:08.216][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:08.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:08.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:08.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:08.222][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:08.223][private$selectFields]
biodb.TRACE[2023-01-28 18:27:08.225][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-01-28 18:27:08.226][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-01-28 18:27:08.227][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:08.229][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:08.230][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:08.231][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:08.233][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:08.234][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:08.236][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:08.237][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:08.238][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:08.240][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:08.241][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:08.242][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:08.244][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:08.245][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:08.246][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:08.248][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-01-28 18:27:08.249][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:08.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:08.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:08.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:08.255][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:08.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:08.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:08.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:08.260][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:08.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:08.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:08.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:08.290][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2023-01-28 18:27:08.292][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:08.293][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:08.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:08.302][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:08.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:08.305][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:08.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:08.308][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:08.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:08.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:08.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:08.313][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:08.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:08.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:08.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:08.319][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:08.320][private$selectFields]
biodb.TRACE[2023-01-28 18:27:08.321][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-01-28 18:27:08.323][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-01-28 18:27:08.324][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:08.326][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:08.327][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:08.328][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:08.330][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:08.331][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:08.332][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:08.334][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:08.335][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:08.337][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:08.338][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:08.339][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:08.341][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:08.342][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:08.343][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:08.345][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-01-28 18:27:08.346][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:08.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:08.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:08.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:08.352][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:08.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:08.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:08.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:08.357][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:08.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:08.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:08.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:08.363][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-01-28 18:27:08.364][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-01-28 18:27:08.366][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-01-28 18:27:08.378][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:08.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:08.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:08.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:08.384][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:08.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:08.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:08.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:08.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:08.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:08.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:08.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:08.395][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:08.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:08.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:08.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:08.485][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:08.486][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:08.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:08.495][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:08.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:08.498][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:08.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:08.570][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:27:08.575][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:27:08.576][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:27:08.579][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-01-28 18:27:09.667][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-01-28 18:27:10.754][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:27:10.764][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2023-01-28 18:27:10.781][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2023-01-28 18:27:10.789][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:27:10.794][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:27:10.795][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:27:10.798][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-01-28 18:27:11.887][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-01-28 18:27:12.987][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:27:12.997][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2023-01-28 18:27:13.012][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2023-01-28 18:27:13.020][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:13.021][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:13.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:13.030][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:13.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:13.033][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:13.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:13.036][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:13.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:13.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.041][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:13.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:13.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.047][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:13.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:13.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:13.052][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:13.054][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:13.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:13.063][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:13.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:13.066][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:13.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:13.068][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:13.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:13.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.074][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:13.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:13.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.080][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:13.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:13.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:13.085][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:13.087][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:13.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:13.096][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:13.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:13.098][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:13.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:13.101][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:13.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:13.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.107][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:13.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:13.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.113][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:13.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:13.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:13.152][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-01-28 18:27:13.186][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:13.187][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:13.188][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:13.196][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:13.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:13.199][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:13.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:13.202][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.207][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.213][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:13.214][private$selectFields]
biodb.TRACE[2023-01-28 18:27:13.215][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-01-28 18:27:13.217][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-01-28 18:27:13.218][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:13.219][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.221][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.222][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.223][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.225][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.226][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.228][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.229][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.230][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:13.232][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:13.233][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.234][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.236][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.237][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.238][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-01-28 18:27:13.240][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.253][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.271][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.277][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2023-01-28 18:27:13.278][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:13.280][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:13.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:13.289][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:13.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:13.292][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:13.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:13.311][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.317][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.352][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:13.353][private$selectFields]
biodb.TRACE[2023-01-28 18:27:13.355][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-01-28 18:27:13.356][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-01-28 18:27:13.357][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:13.359][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.360][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.361][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.363][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.364][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.366][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.367][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.368][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.370][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:13.385][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:13.386][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.388][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.389][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.390][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.392][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-01-28 18:27:13.393][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.399][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.404][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.410][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-01-28 18:27:13.412][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:13.413][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:13.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:13.423][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:13.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:13.425][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:13.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:13.428][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.434][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.440][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:13.441][private$selectFields]
biodb.TRACE[2023-01-28 18:27:13.442][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-01-28 18:27:13.444][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-01-28 18:27:13.445][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:13.447][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.448][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.449][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.451][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.452][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.454][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.455][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.457][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.458][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:13.459][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:13.461][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.462][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.464][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.465][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.467][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-01-28 18:27:13.468][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.474][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.480][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.486][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2023-01-28 18:27:13.487][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-01-28 18:27:13.488][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-01-28 18:27:13.500][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-01-28 18:27:13.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-01-28 18:27:13.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-01-28 18:27:13.507][biodb::testThat]
biodb.INFO [2023-01-28 18:27:13.508][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2023-01-28 18:27:13.510][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-01-28 18:27:13.511][biodb::testThat]
biodb.TRACE[2023-01-28 18:27:13.515][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-01-28 18:27:13.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-01-28 18:27:13.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.521][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:13.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:13.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.527][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:13.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:13.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.533][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:13.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:13.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.538][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:13.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:13.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:13.554][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:13.556][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:13.557][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:13.565][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:13.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:13.568][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:13.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:13.623][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:27:13.627][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-01-28 18:27:13.629][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2023-01-28 18:27:13.631][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-01-28 18:27:13.633][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2023-01-28 18:27:13.636][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:13.637][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:13.639][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:13.647][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:13.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:13.649][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:13.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:13.653][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:13.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:13.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.659][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:13.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:13.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.665][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:13.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:13.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:13.672][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:27:13.676][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-01-28 18:27:13.678][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2023-01-28 18:27:13.680][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-01-28 18:27:13.690][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2023-01-28 18:27:13.694][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:13.695][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:13.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:13.704][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:13.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:13.707][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:13.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:13.710][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:13.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:13.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.716][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:13.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:13.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.722][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:13.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:13.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:13.729][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:27:13.733][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-01-28 18:27:13.735][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba".
biodb.TRACE[2023-01-28 18:27:13.737][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-01-28 18:27:13.739][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content".
biodb.DEBUG[2023-01-28 18:27:13.743][private$bdb$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-01-28 18:27:13.745][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:13.746][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:13.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:13.756][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:13.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:13.758][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:13.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:13.762][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.768][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.774][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:13.775][private$selectFields]
biodb.TRACE[2023-01-28 18:27:13.776][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-01-28 18:27:13.778][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-01-28 18:27:13.779][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:13.781][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.782][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.784][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.785][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.786][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.788][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.789][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.791][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.792][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:13.794][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:13.795][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.797][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.798][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.799][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.801][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-01-28 18:27:13.802][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.808][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.814][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.820][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2023-01-28 18:27:13.822][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:13.823][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:13.824][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:13.832][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:13.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:13.835][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:13.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:13.838][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.844][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.849][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:13.851][private$selectFields]
biodb.TRACE[2023-01-28 18:27:13.852][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-01-28 18:27:13.853][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-01-28 18:27:13.855][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:13.856][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.858][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.859][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.861][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.862][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.864][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.865][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.866][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.868][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:13.869][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:13.871][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.872][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.873][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.875][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.876][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-01-28 18:27:13.878][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.883][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.889][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:13.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.895][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-01-28 18:27:13.897][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-01-28 18:27:13.898][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-01-28 18:27:13.909][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:13.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:13.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.915][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:13.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:13.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.921][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:13.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:13.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:13.926][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:13.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:13.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:13.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:13.942][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:13.943][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:13.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:13.952][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:13.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:13.955][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:13.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:14.010][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:27:14.015][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-01-28 18:27:14.017][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2023-01-28 18:27:14.019][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-01-28 18:27:14.021][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2023-01-28 18:27:14.025][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:27:14.029][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-01-28 18:27:14.031][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2023-01-28 18:27:14.033][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-01-28 18:27:14.035][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2023-01-28 18:27:14.038][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:14.040][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:14.041][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:14.049][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:14.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:14.052][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:14.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:14.055][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:14.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:14.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.060][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:14.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:14.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.066][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:14.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:14.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:14.072][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:14.073][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:14.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:14.082][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:14.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:14.085][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:14.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:14.088][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:14.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:14.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.094][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:14.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:14.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.099][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:14.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:14.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:14.105][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:14.106][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:14.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:14.116][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:14.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:14.118][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:14.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:14.121][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:14.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:14.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.127][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:14.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:14.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.141][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:14.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:14.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:14.147][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-01-28 18:27:14.149][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:14.150][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:14.152][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:14.159][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:14.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:14.162][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:14.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:14.165][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.171][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.176][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:14.178][private$selectFields]
biodb.TRACE[2023-01-28 18:27:14.179][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-01-28 18:27:14.180][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-01-28 18:27:14.182][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:14.183][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.185][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.186][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.187][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.189][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.190][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.192][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.193][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.194][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:14.196][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:14.197][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.198][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.200][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.201][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.202][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-01-28 18:27:14.204][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.209][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.215][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.221][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2023-01-28 18:27:14.223][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:14.224][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:14.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:14.233][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:14.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:14.236][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:14.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:14.239][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.244][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.250][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:14.251][private$selectFields]
biodb.TRACE[2023-01-28 18:27:14.252][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-01-28 18:27:14.254][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-01-28 18:27:14.255][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:14.257][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.258][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.259][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.261][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.262][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.264][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.265][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.266][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.268][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:14.269][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:14.271][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.272][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.273][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.275][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.276][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-01-28 18:27:14.278][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.283][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.289][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.295][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-01-28 18:27:14.297][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:14.298][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:14.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:14.307][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:14.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:14.310][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:14.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:14.313][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.319][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.326][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:14.327][private$selectFields]
biodb.TRACE[2023-01-28 18:27:14.329][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-01-28 18:27:14.330][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-01-28 18:27:14.332][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:14.333][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.335][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.336][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.338][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.339][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.341][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.342][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.343][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.345][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:14.346][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:14.348][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.349][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.351][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.352][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.353][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-01-28 18:27:14.355][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.361][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.366][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.373][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2023-01-28 18:27:14.374][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-01-28 18:27:14.376][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-01-28 18:27:14.387][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-01-28 18:27:14.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-01-28 18:27:14.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-01-28 18:27:14.394][biodb::testThat]
biodb.INFO [2023-01-28 18:27:14.396][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2023-01-28 18:27:14.397][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-01-28 18:27:14.399][biodb::testThat]
biodb.TRACE[2023-01-28 18:27:14.403][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-01-28 18:27:14.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-01-28 18:27:14.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.409][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:14.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:14.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.415][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:14.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:14.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.420][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:14.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:14.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.426][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:14.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:14.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:14.443][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:14.445][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:14.446][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:14.454][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:14.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:14.456][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:14.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:14.512][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:27:14.516][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-01-28 18:27:14.518][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2023-01-28 18:27:14.520][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-01-28 18:27:14.522][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2023-01-28 18:27:14.525][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:14.526][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:14.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:14.536][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:14.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:14.538][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:14.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:14.541][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:14.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:14.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.547][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:14.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:14.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.553][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:14.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:14.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:14.559][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:27:14.564][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-01-28 18:27:14.566][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2023-01-28 18:27:14.567][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-01-28 18:27:14.569][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2023-01-28 18:27:14.572][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:14.582][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:14.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:14.591][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:14.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:14.594][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:14.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:14.597][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:14.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:14.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.602][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:14.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:14.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.608][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:14.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:14.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:14.615][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:27:14.619][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-01-28 18:27:14.621][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba".
biodb.TRACE[2023-01-28 18:27:14.623][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-01-28 18:27:14.625][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content".
biodb.DEBUG[2023-01-28 18:27:14.628][private$bdb$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-01-28 18:27:14.630][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:14.632][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:14.633][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:14.641][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:14.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:14.644][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:14.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:14.646][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.652][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.658][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:14.659][private$selectFields]
biodb.TRACE[2023-01-28 18:27:14.660][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-01-28 18:27:14.662][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-01-28 18:27:14.663][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:14.664][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.666][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.667][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.668][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.670][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.671][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.673][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.674][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.675][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:14.677][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:14.678][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.679][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.681][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.682][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.684][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-01-28 18:27:14.685][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.691][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.696][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.702][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2023-01-28 18:27:14.704][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:14.705][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:14.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:14.714][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:14.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:14.717][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:14.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:14.720][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.725][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.731][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:14.732][private$selectFields]
biodb.TRACE[2023-01-28 18:27:14.734][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-01-28 18:27:14.735][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-01-28 18:27:14.736][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:14.738][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.739][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.740][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.742][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.743][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.745][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.746][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.747][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.749][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:14.750][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:14.752][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.753][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.754][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.756][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.758][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-01-28 18:27:14.759][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.765][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.771][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:14.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.777][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-01-28 18:27:14.779][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-01-28 18:27:14.780][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-01-28 18:27:14.811][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:14.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:14.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.817][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:14.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:14.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.823][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:14.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:14.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.829][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:14.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:14.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:14.848][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:14.849][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:14.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:14.859][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:14.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:14.861][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:14.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:14.919][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:27:14.924][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-01-28 18:27:14.926][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2023-01-28 18:27:14.928][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-01-28 18:27:14.930][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2023-01-28 18:27:14.934][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:27:14.938][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-01-28 18:27:14.940][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2023-01-28 18:27:14.942][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-01-28 18:27:14.944][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2023-01-28 18:27:14.947][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:14.949][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:14.950][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:14.958][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:14.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:14.961][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:14.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:14.964][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:14.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:14.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.969][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:14.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:14.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:14.975][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:14.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:14.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:14.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:14.981][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:14.982][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:14.983][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:14.991][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:14.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:14.994][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:14.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:14.997][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:14.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:15.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:15.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:15.002][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:15.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:15.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:15.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:15.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:15.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:15.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:15.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:15.014][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:15.015][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:15.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:15.033][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:15.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:15.035][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:15.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:15.038][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:15.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:15.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:15.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:15.044][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:15.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:15.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:15.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:15.049][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:15.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:15.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:15.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:15.055][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-01-28 18:27:15.057][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:15.058][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:15.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:15.067][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:15.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:15.070][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:15.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:15.073][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:15.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:15.079][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:15.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:15.084][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:15.085][private$selectFields]
biodb.TRACE[2023-01-28 18:27:15.087][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-01-28 18:27:15.088][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-01-28 18:27:15.089][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:15.091][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.092][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.094][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:15.095][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:15.096][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.098][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.099][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:15.100][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:15.102][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:15.103][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:15.105][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.106][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.108][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:15.109][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:15.110][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-01-28 18:27:15.112][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:15.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:15.118][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:15.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:15.123][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:15.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:15.129][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2023-01-28 18:27:15.131][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:15.132][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:15.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:15.141][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:15.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:15.144][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:15.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:15.147][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:15.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:15.152][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:15.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:15.158][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:15.159][private$selectFields]
biodb.TRACE[2023-01-28 18:27:15.160][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-01-28 18:27:15.162][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-01-28 18:27:15.163][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:15.164][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.166][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.167][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:15.168][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:15.170][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.171][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.173][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:15.174][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:15.175][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:15.177][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:15.178][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.180][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.181][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:15.182][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:15.184][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-01-28 18:27:15.185][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:15.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:15.191][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:15.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:15.197][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:15.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:15.203][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-01-28 18:27:15.205][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:15.206][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:15.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:15.215][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:15.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:15.218][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:15.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:15.221][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:15.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:15.227][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:15.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:15.232][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:15.234][private$selectFields]
biodb.TRACE[2023-01-28 18:27:15.235][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-01-28 18:27:15.236][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-01-28 18:27:15.238][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:15.239][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.240][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.242][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:15.243][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:15.245][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.246][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.247][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:15.249][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:15.250][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:15.251][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-01-28 18:27:15.253][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.254][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.256][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:15.257][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:15.258][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-01-28 18:27:15.260][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:15.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:15.266][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:15.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:15.272][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:15.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:15.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:15.278][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2023-01-28 18:27:15.279][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-01-28 18:27:15.280][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-01-28 18:27:15.311][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-01-28 18:27:15.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-01-28 18:27:15.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:15.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-01-28 18:27:15.318][biodb::testThat]
biodb.INFO [2023-01-28 18:27:15.320][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2023-01-28 18:27:15.321][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-01-28 18:27:15.322][biodb::testThat]
biodb.DEBUG[2023-01-28 18:27:15.325][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2023-01-28 18:27:15.327][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-01-28 18:27:15.329][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2023-01-28 18:27:15.331][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-01-28 18:27:15.332][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-01-28 18:27:15.334][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-01-28 18:27:15.335][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-01-28 18:27:15.336][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-01-28 18:27:15.338][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-01-28 18:27:15.341][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:15.342][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:15.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:15.352][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:15.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:15.355][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:15.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:15.357][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2023-01-28 18:27:15.361][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:27:15.363][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:27:15.365][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2023-01-28 18:27:17.515][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2023-01-28 18:27:18.619][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:27:18.628][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2023-01-28 18:27:18.643][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2023-01-28 18:27:18.671][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2023-01-28 18:27:18.677][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-01-28 18:27:18.696][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-01-28 18:27:18.698][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-01-28 18:27:18.700][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:18.701][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:18.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:18.710][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:18.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:18.713][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:18.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:18.717][ef$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:18.719][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:18.720][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:18.721][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:18.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:18.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:18.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:18.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:18.732][ef$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:27:18.734][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:27:18.735][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:18.737][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:18.738][ef$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:27:18.740][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:27:18.741][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:18.742][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:18.744][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:27:18.746][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:27:18.747][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:18.748][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:18.750][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:27:18.752][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:27:18.753][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:18.754][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:18.756][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:27:18.757][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:27:18.759][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:18.760][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:18.762][ef$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:27:18.763][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:18.764][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:18.766][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:18.767][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:18.769][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:18.770][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:18.771][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:18.773][ef$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:27:18.774][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:27:18.776][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:18.777][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:18.779][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:27:18.780][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:27:18.782][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:18.783][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:18.785][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:27:18.786][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:27:18.787][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:18.789][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:18.790][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:18.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:18.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:18.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:18.799][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:18.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:18.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:18.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:18.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:18.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:18.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:18.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:18.811][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:18.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:18.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:18.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:18.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:18.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:18.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:18.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:18.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:18.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:18.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:18.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:18.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:18.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:18.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:18.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:18.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:18.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:18.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:18.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:18.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:18.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:18.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:18.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:18.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:18.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:18.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:18.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:18.856][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2023-01-28 18:27:18.857][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2023-01-28 18:27:18.866][biodb::testThat]
biodb.INFO [2023-01-28 18:27:18.868][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2023-01-28 18:27:18.869][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-01-28 18:27:18.870][biodb::testThat]
biodb.DEBUG[2023-01-28 18:27:18.885][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2023-01-28 18:27:18.886][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2023-01-28 18:27:18.888][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2023-01-28 18:27:18.890][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2023-01-28 18:27:18.892][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2023-01-28 18:27:18.893][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-01-28 18:27:18.895][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-01-28 18:27:18.896][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-01-28 18:27:18.898][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-01-28 18:27:18.899][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-01-28 18:27:18.905][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:18.906][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:18.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:18.916][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:18.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:18.918][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:18.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:18.921][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2023-01-28 18:27:18.925][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:27:18.927][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:27:18.929][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2023-01-28 18:27:20.044][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2023-01-28 18:27:21.107][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:27:21.117][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2023-01-28 18:27:21.132][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2023-01-28 18:27:21.138][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:21.139][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:21.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:21.148][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:21.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:21.151][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:21.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:21.154][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2023-01-28 18:27:21.157][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:27:21.159][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:27:21.161][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2023-01-28 18:27:22.297][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2023-01-28 18:27:23.530][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:27:23.540][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2023-01-28 18:27:23.555][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2023-01-28 18:27:23.561][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:23.562][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:23.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:23.571][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:23.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:23.573][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:23.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:23.576][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2023-01-28 18:27:23.580][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:27:23.582][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:27:23.584][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2023-01-28 18:27:24.695][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2023-01-28 18:27:25.888][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:27:25.897][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2023-01-28 18:27:25.913][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2023-01-28 18:27:25.927][private$doSaveContentToFile] Saving to cache [3]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2023-01-28 18:27:25.932][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-01-28 18:27:25.954][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2023-01-28 18:27:25.955][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2023-01-28 18:27:25.957][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:25.958][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:25.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:25.967][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:25.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:25.970][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:25.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:25.974][ef$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:25.975][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:25.977][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:25.978][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:25.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:25.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:25.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:25.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:25.989][ef$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:27:25.990][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:27:25.991][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:25.993][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:25.994][ef$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:27:25.996][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:27:25.997][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:25.998][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.000][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:27:26.002][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:27:26.003][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.004][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.006][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:27:26.007][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:27:26.009][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.010][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.011][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:27:26.013][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:27:26.014][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.015][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.017][ef$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:27:26.018][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:26.020][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.021][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.023][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:26.024][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:26.025][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.027][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.028][ef$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:27:26.030][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:27:26.031][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.032][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.034][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:27:26.036][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:27:26.037][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.038][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.040][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:27:26.041][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:27:26.043][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.044][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.046][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:26.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:26.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.051][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:26.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:26.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.057][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:26.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:26.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.062][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:26.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:26.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:26.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:26.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:26.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:26.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:26.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:26.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:26.087][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:26.089][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:26.090][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:26.098][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:26.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:26.100][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:26.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:26.104][ef$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:26.106][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:26.107][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.108][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:26.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:26.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.119][ef$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:27:26.121][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:27:26.122][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.123][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.125][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:27:26.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:27:26.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.134][ef$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:27:26.135][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:27:26.137][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.138][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.140][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:27:26.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:27:26.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.149][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:27:26.150][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:27:26.152][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.153][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.155][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:27:26.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:27:26.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.164][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:27:26.165][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:27:26.167][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.168][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.170][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:27:26.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:27:26.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.179][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:27:26.180][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:27:26.182][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.183][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.185][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:27:26.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:27:26.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.194][ef$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:27:26.195][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:26.211][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.213][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.217][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:27:26.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:26.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.226][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:26.228][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:26.229][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.230][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.232][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:26.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:26.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.241][ef$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:27:26.243][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:27:26.244][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.245][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.247][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:27:26.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:27:26.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.257][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:27:26.258][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:27:26.260][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.261][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.263][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:27:26.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:27:26.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.272][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:27:26.274][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:27:26.275][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.276][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.278][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:27:26.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:27:26.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.287][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:26.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:26.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.293][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:26.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:26.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:26.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:26.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.304][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:26.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:26.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:26.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:26.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:26.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:26.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:26.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:26.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:26.330][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:26.331][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:26.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:26.340][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:26.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:26.342][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:26.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:26.346][ef$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:26.348][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:26.349][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.350][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.352][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:26.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:26.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.361][ef$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:27:26.362][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:27:26.364][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.365][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.367][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:27:26.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:27:26.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.376][ef$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:27:26.377][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:27:26.379][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.380][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.382][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:27:26.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:27:26.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.391][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:27:26.392][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:27:26.394][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.395][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.397][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:27:26.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:27:26.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.406][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:27:26.407][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:27:26.409][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.410][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.412][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:27:26.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:27:26.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.421][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:27:26.425][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:27:26.426][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.436][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.438][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:27:26.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:27:26.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.451][ef$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:27:26.453][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:26.454][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.455][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.457][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:27:26.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:26.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.467][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:26.468][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:26.470][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.471][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.473][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:26.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:26.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.482][ef$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:27:26.484][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:27:26.485][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.486][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.488][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:27:26.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:27:26.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.497][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:27:26.499][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:27:26.500][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.501][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.503][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:27:26.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:27:26.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.512][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:27:26.514][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:27:26.515][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.516][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.518][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:27:26.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:27:26.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.527][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:26.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:26.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.532][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:26.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:26.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:26.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:26.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.543][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:26.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:26.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:26.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:26.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:26.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:26.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:26.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:26.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:26.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:26.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:26.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:26.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:26.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:26.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:26.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:26.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:26.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:26.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:26.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:26.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:26.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:26.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:26.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:26.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:26.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:26.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:26.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:26.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:26.620][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2023-01-28 18:27:26.622][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2023-01-28 18:27:26.623][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2023-01-28 18:27:26.639][biodb::testThat]
biodb.INFO [2023-01-28 18:27:26.640][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2023-01-28 18:27:26.642][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-01-28 18:27:26.643][biodb::testThat]
biodb.INFO [2023-01-28 18:27:26.682][biodb::testThat]
biodb.INFO [2023-01-28 18:27:26.683][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2023-01-28 18:27:26.685][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-01-28 18:27:26.686][biodb::testThat]
biodb.INFO [2023-01-28 18:27:26.695][biodb::testThat]
biodb.INFO [2023-01-28 18:27:26.697][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2023-01-28 18:27:26.698][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-01-28 18:27:26.699][biodb::testThat]
biodb.DEBUG[2023-01-28 18:27:26.703][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:27:26.707][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:27:26.709][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:27:26.711][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2023-01-28 18:27:27.893][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2023-01-28 18:27:29.559][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:27:29.569][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2023-01-28 18:27:29.585][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2023-01-28 18:27:29.609][ef$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:27:29.610][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:27:29.611][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:29.613][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:29.614][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:29.615][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:29.617][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:29.618][ef$get] fields variable is a list.
biodb.INFO [2023-01-28 18:27:29.620][biodb::testThat]
biodb.INFO [2023-01-28 18:27:29.621][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2023-01-28 18:27:29.622][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-01-28 18:27:29.623][biodb::testThat]
biodb.ERROR[2023-01-28 18:27:29.641][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2023-01-28 18:27:29.661][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2023-01-28 18:27:29.674][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-01-28 18:27:29.676][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-01-28 18:27:29.677][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-01-28 18:27:29.678][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-01-28 18:27:29.680][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:29.681][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:29.682][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:29.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:29.684][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:29.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-01-28 18:27:29.700][biodb::testContext]
biodb.INFO [2023-01-28 18:27:29.702][biodb::testContext] ********************************************************************************
biodb.INFO [2023-01-28 18:27:29.703][biodb::testContext] Test context - Test conversions
biodb.INFO [2023-01-28 18:27:29.704][biodb::testContext] ********************************************************************************
biodb.INFO [2023-01-28 18:27:29.705][biodb::testContext]
biodb.INFO [2023-01-28 18:27:29.712][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-01-28 18:27:29.714][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-01-28 18:27:29.718][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-01-28 18:27:29.720][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-01-28 18:27:29.721][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-01-28 18:27:29.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:29.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:29.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:29.726][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-01-28 18:27:29.728][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-01-28 18:27:29.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:29.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:29.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:29.733][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-01-28 18:27:29.734][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-01-28 18:27:29.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:29.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:29.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:29.739][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-01-28 18:27:29.740][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-01-28 18:27:29.742][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-01-28 18:27:29.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:29.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:29.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:29.747][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-01-28 18:27:29.748][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-01-28 18:27:29.749][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-01-28 18:27:29.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:29.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:29.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:29.754][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-01-28 18:27:29.756][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-01-28 18:27:29.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:29.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:29.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:29.761][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-01-28 18:27:29.762][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-01-28 18:27:29.764][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-01-28 18:27:29.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:29.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:29.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:29.769][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-01-28 18:27:29.770][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-01-28 18:27:29.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:29.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:29.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:29.775][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-01-28 18:27:29.776][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-01-28 18:27:29.778][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-01-28 18:27:29.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:29.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:29.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:29.783][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-01-28 18:27:29.784][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-01-28 18:27:29.785][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-01-28 18:27:29.787][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-01-28 18:27:29.788][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-01-28 18:27:29.790][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-01-28 18:27:29.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:29.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:29.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:29.794][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-01-28 18:27:29.796][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-01-28 18:27:29.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:29.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:29.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:29.801][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-01-28 18:27:29.802][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-01-28 18:27:29.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:29.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:29.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:29.807][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-01-28 18:27:29.809][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-01-28 18:27:29.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:29.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:29.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:29.814][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-01-28 18:27:29.815][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-01-28 18:27:29.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:29.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:29.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:29.820][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-01-28 18:27:29.822][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-01-28 18:27:29.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:29.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:29.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:29.826][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-01-28 18:27:29.828][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-01-28 18:27:29.832][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-01-28 18:27:29.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:29.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:29.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:29.837][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-01-28 18:27:29.839][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-01-28 18:27:29.840][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-01-28 18:27:29.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:29.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:29.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:29.845][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-01-28 18:27:29.848][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:29.849][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-01-28 18:27:29.850][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:29.852][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-01-28 18:27:29.853][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:29.855][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-01-28 18:27:29.856][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:29.859][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-01-28 18:27:29.860][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-01-28 18:27:29.862][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-01-28 18:27:29.863][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:29.865][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-01-28 18:27:29.866][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-01-28 18:27:29.867][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:29.869][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:29.870][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-01-28 18:27:29.870][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-01-28 18:27:29.870][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-01-28 18:27:29.870][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-01-28 18:27:29.870][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-01-28 18:27:29.888][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-01-28 18:27:29.889][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:27:29.890][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:27:29.892][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-01-28 18:27:29.893][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:27:29.894][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:27:29.896][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-01-28 18:27:29.897][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:29.898][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-01-28 18:27:29.899][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-01-28 18:27:29.900][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:29.902][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:29.903][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-01-28 18:27:29.906][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:29.907][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-01-28 18:27:29.909][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:29.910][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-01-28 18:27:29.911][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:29.913][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-01-28 18:27:29.914][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:29.915][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-01-28 18:27:29.917][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-01-28 18:27:29.918][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-01-28 18:27:29.919][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:29.921][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-01-28 18:27:29.922][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-01-28 18:27:29.923][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:29.925][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:29.926][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-01-28 18:27:29.926][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-01-28 18:27:29.926][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-01-28 18:27:29.926][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-01-28 18:27:29.926][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-01-28 18:27:29.927][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-01-28 18:27:29.928][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:27:29.930][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:27:29.931][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-01-28 18:27:29.932][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:27:29.933][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:27:29.935][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-01-28 18:27:29.936][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:29.937][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-01-28 18:27:29.938][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-01-28 18:27:29.940][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:29.941][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:29.943][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-01-28 18:27:29.945][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:29.946][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-01-28 18:27:29.948][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:29.949][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-01-28 18:27:29.950][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:29.952][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-01-28 18:27:29.953][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:29.954][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-01-28 18:27:29.956][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-01-28 18:27:29.957][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-01-28 18:27:29.958][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:29.960][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-01-28 18:27:29.961][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-01-28 18:27:29.963][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:29.964][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:29.965][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:29.967][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-01-28 18:27:29.968][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:27:29.969][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:27:29.970][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-01-28 18:27:29.972][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:27:29.973][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:27:29.974][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-01-28 18:27:29.976][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:29.977][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-01-28 18:27:29.978][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-01-28 18:27:29.979][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:29.981][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:29.982][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-01-28 18:27:29.985][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:29.986][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-01-28 18:27:29.987][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:29.989][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-01-28 18:27:29.990][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:29.991][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-01-28 18:27:29.993][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:29.994][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-01-28 18:27:29.995][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-01-28 18:27:29.997][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-01-28 18:27:29.998][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:29.999][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-01-28 18:27:30.001][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-01-28 18:27:30.002][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:30.003][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:30.005][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:30.006][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-01-28 18:27:30.007][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:27:30.009][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:27:30.010][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-01-28 18:27:30.011][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:27:30.012][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:27:30.014][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-01-28 18:27:30.015][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:30.016][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-01-28 18:27:30.017][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-01-28 18:27:30.019][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:30.020][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:30.022][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-01-28 18:27:30.023][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:30.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:30.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:30.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:30.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:30.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:30.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:30.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:30.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:30.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:30.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:30.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:30.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:30.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:30.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:30.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:30.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:30.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:30.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:30.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:30.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:30.048][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.DEBUG[2023-01-28 18:27:30.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:30.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:30.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:30.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:30.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:30.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:30.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:30.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:30.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:30.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:30.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:30.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:30.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:30.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:30.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:30.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:30.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:30.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:30.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:30.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:30.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:30.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:30.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:30.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:30.079][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[2023-01-28 18:27:30.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:30.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:30.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:30.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:30.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:30.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:30.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:30.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:30.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:30.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:30.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:30.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:30.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:30.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:30.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:30.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:30.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:30.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:30.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:30.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:30.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:30.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:30.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:30.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:30.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:30.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:30.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:30.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:30.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:30.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:30.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:30.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:30.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:30.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:30.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:30.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:30.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:30.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:30.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:30.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:30.129][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-01-28 18:27:30.131][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-01-28 18:27:30.133][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-01-28 18:27:30.135][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-01-28 18:27:30.137][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-01-28 18:27:30.139][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-01-28 18:27:30.141][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-01-28 18:27:30.143][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-01-28 18:27:30.145][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-01-28 18:27:30.147][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-01-28 18:27:30.149][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-01-28 18:27:30.151][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-01-28 18:27:30.153][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-01-28 18:27:30.155][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-01-28 18:27:30.157][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-01-28 18:27:30.158][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-01-28 18:27:30.160][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-01-28 18:27:30.162][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-01-28 18:27:30.164][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-01-28 18:27:30.166][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-01-28 18:27:30.168][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-01-28 18:27:30.170][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-01-28 18:27:30.172][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-01-28 18:27:30.174][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-01-28 18:27:30.176][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-01-28 18:27:30.178][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-01-28 18:27:30.180][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-01-28 18:27:30.182][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-01-28 18:27:30.184][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-01-28 18:27:30.186][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-01-28 18:27:30.188][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-01-28 18:27:30.190][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-01-28 18:27:30.192][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-01-28 18:27:30.194][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-01-28 18:27:30.196][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-01-28 18:27:30.198][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-01-28 18:27:30.200][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-01-28 18:27:30.201][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-01-28 18:27:30.203][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-01-28 18:27:30.205][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-01-28 18:27:30.207][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-01-28 18:27:30.209][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-01-28 18:27:30.211][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-01-28 18:27:30.213][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-01-28 18:27:30.215][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-01-28 18:27:30.217][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-01-28 18:27:30.219][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-01-28 18:27:30.223][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-01-28 18:27:30.225][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-01-28 18:27:30.227][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-01-28 18:27:30.229][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-01-28 18:27:30.231][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-01-28 18:27:30.233][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-01-28 18:27:30.235][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-01-28 18:27:30.237][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-01-28 18:27:30.239][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-01-28 18:27:30.241][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-01-28 18:27:30.243][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-01-28 18:27:30.245][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-01-28 18:27:30.247][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-01-28 18:27:30.249][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-01-28 18:27:30.251][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-01-28 18:27:30.253][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-01-28 18:27:30.254][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-01-28 18:27:30.256][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-01-28 18:27:30.258][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-01-28 18:27:30.260][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-01-28 18:27:30.262][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-01-28 18:27:30.264][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-01-28 18:27:30.266][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-01-28 18:27:30.268][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-01-28 18:27:30.270][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-01-28 18:27:30.272][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-01-28 18:27:30.274][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-01-28 18:27:30.276][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-01-28 18:27:30.278][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-01-28 18:27:30.279][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-01-28 18:27:30.281][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-01-28 18:27:30.283][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-01-28 18:27:30.285][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-01-28 18:27:30.296][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-01-28 18:27:30.298][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-01-28 18:27:30.301][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-01-28 18:27:30.303][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-01-28 18:27:30.305][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-01-28 18:27:30.306][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-01-28 18:27:30.307][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:30.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:30.310][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:30.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:30.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:30.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:30.314][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:30.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:30.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:30.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:30.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:30.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:30.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:30.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:30.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:30.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:30.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:30.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:30.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:30.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:30.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:30.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:30.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:30.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:30.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:30.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:30.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:30.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:30.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:30.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:30.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:30.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:30.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:30.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:30.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:30.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:30.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:30.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:30.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:30.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:30.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:30.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:30.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:30.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:30.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:30.360][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[2023-01-28 18:27:30.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:30.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:30.364][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:30.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:30.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:30.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:30.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:30.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:30.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:30.372][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:30.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:30.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:30.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:30.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:30.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:30.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:30.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:30.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:30.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:30.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:30.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:30.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:30.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:30.388][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:30.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:30.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:30.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:30.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:30.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:30.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:30.397][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:30.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:30.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:30.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:30.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:30.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:30.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:30.405][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:30.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:30.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:30.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:30.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:30.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:30.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:30.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:30.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:30.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:30.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:30.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:30.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:30.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:30.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:30.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:30.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:30.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:30.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:30.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:30.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:30.430][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:30.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:30.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:30.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:30.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:30.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:30.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:30.438][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:30.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:30.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:30.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:30.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:30.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:30.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:30.446][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:30.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:30.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:30.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:30.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:30.453][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-01-28 18:27:30.455][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-01-28 18:27:30.458][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:30.459][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-01-28 18:27:30.461][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:30.462][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-01-28 18:27:30.463][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:30.465][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-01-28 18:27:30.466][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:30.467][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-01-28 18:27:30.469][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-01-28 18:27:30.470][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-01-28 18:27:30.472][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:30.473][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-01-28 18:27:30.474][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-01-28 18:27:30.476][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-01-28 18:27:30.476][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-01-28 18:27:30.476][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-01-28 18:27:30.476][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-01-28 18:27:30.476][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-01-28 18:27:30.476][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-01-28 18:27:30.476][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-01-28 18:27:30.476][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-01-28 18:27:30.476][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-01-28 18:27:30.476][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-01-28 18:27:30.476][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-01-28 18:27:30.477][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:30.479][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-01-28 18:27:30.479][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-01-28 18:27:30.479][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-01-28 18:27:30.480][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-01-28 18:27:30.481][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:27:30.482][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:27:30.484][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-01-28 18:27:30.485][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:27:30.486][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:27:30.488][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-01-28 18:27:30.489][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-01-28 18:27:30.489][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-01-28 18:27:30.490][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-01-28 18:27:30.492][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-01-28 18:27:30.493][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:30.494][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-01-28 18:27:30.494][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-01-28 18:27:30.496][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-01-28 18:27:30.498][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-01-28 18:27:30.500][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-01-28 18:27:30.502][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-01-28 18:27:30.504][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-01-28 18:27:30.507][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-01-28 18:27:30.511][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-01-28 18:27:30.512][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-01-28 18:27:30.514][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-01-28 18:27:30.516][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-01-28 18:27:30.518][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-01-28 18:27:30.519][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-01-28 18:27:30.521][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-01-28 18:27:30.522][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-01-28 18:27:30.524][biodb::testThat]
biodb.INFO [2023-01-28 18:27:30.526][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2023-01-28 18:27:30.527][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-01-28 18:27:30.528][biodb::testThat]
biodb.DEBUG[2023-01-28 18:27:30.533][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-01-28 18:27:30.539][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:27:30.540][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:27:30.542][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2023-01-28 18:27:31.715][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2023-01-28 18:27:33.080][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:27:33.089][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2023-01-28 18:27:33.109][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2023-01-28 18:27:33.127][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:27:33.131][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:27:33.133][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:27:33.135][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-01-28 18:27:34.243][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-01-28 18:27:38.992][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:27:39.023][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2023-01-28 18:27:39.039][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2023-01-28 18:27:39.045][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:39.046][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:39.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:39.055][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:39.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:39.058][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:39.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:39.062][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:27:39.066][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:27:39.068][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:27:39.070][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-01-28 18:27:40.795][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-01-28 18:27:41.921][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:27:41.947][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2023-01-28 18:27:41.962][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2023-01-28 18:27:41.969][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:41.970][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:41.971][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:41.979][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:41.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:41.981][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:41.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:42.004][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:42.005][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:42.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:42.014][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:42.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:42.016][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:42.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:42.023][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:27:42.027][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-01-28 18:27:42.029][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2023-01-28 18:27:42.031][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-01-28 18:27:42.032][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2023-01-28 18:27:42.035][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:42.036][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:42.037][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:42.044][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:42.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:42.047][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:42.048][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.DEBUG[2023-01-28 18:27:42.051][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:27:42.055][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-01-28 18:27:42.057][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2023-01-28 18:27:42.058][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-01-28 18:27:42.060][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2023-01-28 18:27:42.063][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:42.064][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:42.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:42.073][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:42.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:42.078][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:42.079][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[2023-01-28 18:27:42.081][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:42.082][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:42.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:42.091][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:42.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:42.093][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:42.095][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[2023-01-28 18:27:42.099][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:27:42.103][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-01-28 18:27:42.105][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2023-01-28 18:27:42.107][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-01-28 18:27:42.109][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2023-01-28 18:27:42.111][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:42.112][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:42.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:42.121][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:42.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:42.123][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:42.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:42.127][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:27:42.131][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-01-28 18:27:42.133][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2023-01-28 18:27:42.135][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-01-28 18:27:42.137][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2023-01-28 18:27:42.139][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:42.140][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:42.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:42.149][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:42.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:42.151][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:42.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:42.155][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:27:42.159][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:27:42.161][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:27:42.163][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-01-28 18:27:43.289][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-01-28 18:27:44.430][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:27:44.441][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2023-01-28 18:27:44.458][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2023-01-28 18:27:44.487][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:44.488][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:44.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:44.497][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:44.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:44.499][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:44.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-01-28 18:27:44.505][biodb::testThat]
biodb.INFO [2023-01-28 18:27:44.507][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2023-01-28 18:27:44.509][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-01-28 18:27:44.510][biodb::testThat]
biodb.DEBUG[2023-01-28 18:27:44.515][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:27:44.520][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:27:44.521][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:27:44.524][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-01-28 18:27:46.480][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-01-28 18:27:47.588][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:27:47.598][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2023-01-28 18:27:47.618][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2023-01-28 18:27:47.624][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:47.626][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:47.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:47.635][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:47.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:47.638][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:47.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:47.644][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:27:47.648][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:27:47.650][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:27:47.652][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-01-28 18:27:48.718][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-01-28 18:27:49.828][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:27:49.838][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2023-01-28 18:27:49.854][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2023-01-28 18:27:49.861][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:49.863][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:49.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:49.872][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:49.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:49.875][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:49.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-01-28 18:27:49.880][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-01-28 18:27:49.881][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-01-28 18:27:49.883][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-01-28 18:27:49.884][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-01-28 18:27:49.885][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:49.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:49.888][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:49.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:49.891][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:49.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-01-28 18:27:49.898][biodb::testContext]
biodb.INFO [2023-01-28 18:27:49.899][biodb::testContext] ********************************************************************************
biodb.INFO [2023-01-28 18:27:49.901][biodb::testContext] Test context - Test web services
biodb.INFO [2023-01-28 18:27:49.902][biodb::testContext] ********************************************************************************
biodb.INFO [2023-01-28 18:27:49.903][biodb::testContext]
biodb.INFO [2023-01-28 18:27:49.910][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-01-28 18:27:49.912][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-01-28 18:27:49.917][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-01-28 18:27:49.919][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-01-28 18:27:49.920][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-01-28 18:27:49.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:49.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:49.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:49.925][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-01-28 18:27:49.927][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-01-28 18:27:49.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:49.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:49.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:49.932][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-01-28 18:27:49.934][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-01-28 18:27:49.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:49.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:49.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:49.939][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-01-28 18:27:49.940][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-01-28 18:27:49.942][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-01-28 18:27:49.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:49.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:49.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:49.947][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-01-28 18:27:49.949][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-01-28 18:27:49.950][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-01-28 18:27:49.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:49.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:49.954][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[2023-01-28 18:27:49.955][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-01-28 18:27:49.957][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-01-28 18:27:49.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:49.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:49.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:49.962][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-01-28 18:27:49.964][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-01-28 18:27:49.965][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-01-28 18:27:49.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:49.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:49.970][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[2023-01-28 18:27:49.971][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-01-28 18:27:49.973][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-01-28 18:27:49.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:49.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:49.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:49.978][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-01-28 18:27:49.980][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-01-28 18:27:49.981][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-01-28 18:27:49.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:49.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:49.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:49.987][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-01-28 18:27:49.988][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-01-28 18:27:49.990][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-01-28 18:27:49.991][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-01-28 18:27:49.993][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-01-28 18:27:49.994][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-01-28 18:27:49.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:49.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:49.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.000][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-01-28 18:27:50.001][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-01-28 18:27:50.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.007][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-01-28 18:27:50.009][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-01-28 18:27:50.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.014][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-01-28 18:27:50.016][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-01-28 18:27:50.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.021][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-01-28 18:27:50.023][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-01-28 18:27:50.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.028][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-01-28 18:27:50.030][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-01-28 18:27:50.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.035][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-01-28 18:27:50.037][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-01-28 18:27:50.042][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-01-28 18:27:50.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.048][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-01-28 18:27:50.073][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-01-28 18:27:50.075][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-01-28 18:27:50.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.081][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-01-28 18:27:50.084][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:50.085][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-01-28 18:27:50.087][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:50.088][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-01-28 18:27:50.090][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:50.091][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-01-28 18:27:50.093][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:50.094][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-01-28 18:27:50.096][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-01-28 18:27:50.097][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-01-28 18:27:50.099][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:50.100][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-01-28 18:27:50.101][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-01-28 18:27:50.103][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:50.104][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:50.106][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-01-28 18:27:50.106][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-01-28 18:27:50.106][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-01-28 18:27:50.106][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-01-28 18:27:50.106][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-01-28 18:27:50.107][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-01-28 18:27:50.108][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:27:50.110][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:27:50.111][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-01-28 18:27:50.112][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:27:50.113][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:27:50.115][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-01-28 18:27:50.116][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:50.117][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-01-28 18:27:50.119][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-01-28 18:27:50.120][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:50.121][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:50.123][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-01-28 18:27:50.125][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:50.127][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-01-28 18:27:50.128][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:50.130][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-01-28 18:27:50.131][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:50.132][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-01-28 18:27:50.134][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:50.135][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-01-28 18:27:50.136][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-01-28 18:27:50.138][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-01-28 18:27:50.139][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:50.140][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-01-28 18:27:50.142][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-01-28 18:27:50.143][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:50.145][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:50.146][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-01-28 18:27:50.146][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-01-28 18:27:50.146][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-01-28 18:27:50.146][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-01-28 18:27:50.146][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-01-28 18:27:50.147][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-01-28 18:27:50.149][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:27:50.150][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:27:50.151][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-01-28 18:27:50.153][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:27:50.154][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:27:50.155][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-01-28 18:27:50.157][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:50.158][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-01-28 18:27:50.159][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-01-28 18:27:50.160][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:50.162][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:50.163][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-01-28 18:27:50.166][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:50.167][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-01-28 18:27:50.169][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:50.170][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-01-28 18:27:50.171][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:50.173][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-01-28 18:27:50.174][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:50.175][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-01-28 18:27:50.177][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-01-28 18:27:50.178][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-01-28 18:27:50.180][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:50.181][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-01-28 18:27:50.182][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-01-28 18:27:50.184][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:50.185][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:50.186][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:50.188][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-01-28 18:27:50.189][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:27:50.190][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:27:50.192][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-01-28 18:27:50.193][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:27:50.194][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:27:50.196][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-01-28 18:27:50.197][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:50.198][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-01-28 18:27:50.199][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-01-28 18:27:50.201][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:50.202][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:50.204][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-01-28 18:27:50.206][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:50.208][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-01-28 18:27:50.209][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:50.210][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-01-28 18:27:50.212][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:50.213][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-01-28 18:27:50.215][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:50.216][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-01-28 18:27:50.217][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-01-28 18:27:50.219][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-01-28 18:27:50.220][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:50.221][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-01-28 18:27:50.223][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-01-28 18:27:50.224][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:50.226][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:50.227][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:50.228][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-01-28 18:27:50.230][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:27:50.231][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:27:50.232][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-01-28 18:27:50.233][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:27:50.235][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:27:50.236][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-01-28 18:27:50.237][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:50.239][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-01-28 18:27:50.240][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-01-28 18:27:50.241][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:50.243][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:50.244][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-01-28 18:27:50.246][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:50.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:50.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:50.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:50.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:50.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:50.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:50.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:50.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:50.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:50.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:50.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:50.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:50.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:50.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:50.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:50.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:50.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:50.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:50.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:50.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:50.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:50.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:50.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:50.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:50.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:50.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:50.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:50.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:50.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:50.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:50.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:50.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:50.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:50.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.357][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-01-28 18:27:50.359][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-01-28 18:27:50.361][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-01-28 18:27:50.363][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-01-28 18:27:50.365][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-01-28 18:27:50.367][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-01-28 18:27:50.369][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-01-28 18:27:50.371][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-01-28 18:27:50.373][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-01-28 18:27:50.375][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-01-28 18:27:50.377][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-01-28 18:27:50.379][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-01-28 18:27:50.381][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-01-28 18:27:50.383][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-01-28 18:27:50.385][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-01-28 18:27:50.387][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-01-28 18:27:50.389][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-01-28 18:27:50.391][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-01-28 18:27:50.393][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-01-28 18:27:50.395][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-01-28 18:27:50.397][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-01-28 18:27:50.399][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-01-28 18:27:50.401][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-01-28 18:27:50.403][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-01-28 18:27:50.405][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-01-28 18:27:50.407][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-01-28 18:27:50.409][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-01-28 18:27:50.411][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-01-28 18:27:50.413][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-01-28 18:27:50.415][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-01-28 18:27:50.417][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-01-28 18:27:50.419][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-01-28 18:27:50.421][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-01-28 18:27:50.423][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-01-28 18:27:50.425][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-01-28 18:27:50.427][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-01-28 18:27:50.429][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-01-28 18:27:50.431][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-01-28 18:27:50.433][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-01-28 18:27:50.435][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-01-28 18:27:50.437][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-01-28 18:27:50.439][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-01-28 18:27:50.441][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-01-28 18:27:50.443][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-01-28 18:27:50.445][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-01-28 18:27:50.447][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-01-28 18:27:50.449][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-01-28 18:27:50.451][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-01-28 18:27:50.453][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-01-28 18:27:50.455][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-01-28 18:27:50.457][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-01-28 18:27:50.459][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-01-28 18:27:50.461][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-01-28 18:27:50.463][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-01-28 18:27:50.465][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-01-28 18:27:50.467][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-01-28 18:27:50.469][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-01-28 18:27:50.471][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-01-28 18:27:50.473][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-01-28 18:27:50.475][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-01-28 18:27:50.477][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-01-28 18:27:50.479][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-01-28 18:27:50.489][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-01-28 18:27:50.491][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-01-28 18:27:50.494][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-01-28 18:27:50.496][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-01-28 18:27:50.498][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-01-28 18:27:50.500][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-01-28 18:27:50.501][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-01-28 18:27:50.503][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-01-28 18:27:50.505][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-01-28 18:27:50.507][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-01-28 18:27:50.509][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-01-28 18:27:50.511][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-01-28 18:27:50.513][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-01-28 18:27:50.515][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-01-28 18:27:50.517][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-01-28 18:27:50.519][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-01-28 18:27:50.521][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-01-28 18:27:50.523][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-01-28 18:27:50.525][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-01-28 18:27:50.527][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-01-28 18:27:50.529][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-01-28 18:27:50.531][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-01-28 18:27:50.533][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-01-28 18:27:50.534][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-01-28 18:27:50.536][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:50.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:50.538][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:50.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:50.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:50.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:50.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.548][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[2023-01-28 18:27:50.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:50.551][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:50.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:50.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:50.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:50.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:50.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:50.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:50.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:50.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:50.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:50.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:50.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:50.577][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:50.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:50.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:50.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:50.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:50.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:50.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:50.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:50.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:50.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:50.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:50.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:50.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:50.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:50.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:50.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:50.612][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:50.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:50.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:50.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:50.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:50.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:50.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:50.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:50.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:50.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:50.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:50.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:50.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:50.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:50.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:50.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:50.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:50.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:50.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:50.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:50.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:50.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:50.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:50.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:50.676][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:50.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:50.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:50.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:50.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:50.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:50.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:50.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:50.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:50.694][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:50.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:50.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:50.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:50.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:50.701][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-01-28 18:27:50.703][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-01-28 18:27:50.706][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:50.707][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-01-28 18:27:50.708][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:50.710][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-01-28 18:27:50.711][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:50.713][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-01-28 18:27:50.714][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:50.716][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-01-28 18:27:50.717][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-01-28 18:27:50.718][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-01-28 18:27:50.720][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:50.721][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-01-28 18:27:50.723][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-01-28 18:27:50.724][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-01-28 18:27:50.724][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-01-28 18:27:50.724][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-01-28 18:27:50.724][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-01-28 18:27:50.724][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-01-28 18:27:50.724][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-01-28 18:27:50.724][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-01-28 18:27:50.724][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-01-28 18:27:50.724][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-01-28 18:27:50.724][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-01-28 18:27:50.724][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-01-28 18:27:50.726][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:50.727][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-01-28 18:27:50.727][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-01-28 18:27:50.727][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-01-28 18:27:50.729][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-01-28 18:27:50.730][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:27:50.732][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:27:50.733][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-01-28 18:27:50.734][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:27:50.736][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:27:50.737][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-01-28 18:27:50.739][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-01-28 18:27:50.739][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-01-28 18:27:50.740][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-01-28 18:27:50.741][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-01-28 18:27:50.743][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:50.744][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-01-28 18:27:50.744][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-01-28 18:27:50.746][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-01-28 18:27:50.749][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-01-28 18:27:50.751][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-01-28 18:27:50.753][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-01-28 18:27:50.755][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-01-28 18:27:50.758][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-01-28 18:27:50.762][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-01-28 18:27:50.764][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-01-28 18:27:50.766][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-01-28 18:27:50.768][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-01-28 18:27:50.770][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-01-28 18:27:50.771][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-01-28 18:27:50.773][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-01-28 18:27:50.775][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-01-28 18:27:50.776][biodb::testThat]
biodb.INFO [2023-01-28 18:27:50.778][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2023-01-28 18:27:50.779][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-01-28 18:27:50.781][biodb::testThat]
biodb.DEBUG[2023-01-28 18:27:50.785][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-01-28 18:27:50.790][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-01-28 18:27:50.792][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2023-01-28 18:27:50.794][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-01-28 18:27:50.796][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2023-01-28 18:27:50.801][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:27:50.806][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:27:50.807][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:27:50.809][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-01-28 18:27:51.912][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-01-28 18:27:54.093][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:27:54.102][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2023-01-28 18:27:54.117][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2023-01-28 18:27:54.126][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-01-28 18:27:54.128][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-01-28 18:27:54.129][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-01-28 18:27:54.130][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-01-28 18:27:54.132][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:54.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:54.134][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:54.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:54.137][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-01-28 18:27:54.159][biodb::testContext]
biodb.INFO [2023-01-28 18:27:54.161][biodb::testContext] ********************************************************************************
biodb.INFO [2023-01-28 18:27:54.162][biodb::testContext] Test context - Non regression tests
biodb.INFO [2023-01-28 18:27:54.164][biodb::testContext] ********************************************************************************
biodb.INFO [2023-01-28 18:27:54.165][biodb::testContext]
biodb.INFO [2023-01-28 18:27:54.171][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-01-28 18:27:54.173][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-01-28 18:27:54.178][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-01-28 18:27:54.179][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-01-28 18:27:54.181][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-01-28 18:27:54.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.186][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-01-28 18:27:54.188][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-01-28 18:27:54.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.193][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-01-28 18:27:54.194][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-01-28 18:27:54.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.199][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-01-28 18:27:54.201][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-01-28 18:27:54.202][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-01-28 18:27:54.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.207][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-01-28 18:27:54.209][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-01-28 18:27:54.210][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-01-28 18:27:54.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.215][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-01-28 18:27:54.217][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-01-28 18:27:54.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.222][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-01-28 18:27:54.223][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-01-28 18:27:54.224][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-01-28 18:27:54.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.229][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-01-28 18:27:54.231][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-01-28 18:27:54.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.236][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-01-28 18:27:54.237][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-01-28 18:27:54.239][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-01-28 18:27:54.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.244][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-01-28 18:27:54.245][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-01-28 18:27:54.247][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-01-28 18:27:54.248][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-01-28 18:27:54.249][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-01-28 18:27:54.251][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-01-28 18:27:54.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.256][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-01-28 18:27:54.257][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-01-28 18:27:54.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.263][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-01-28 18:27:54.264][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-01-28 18:27:54.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.269][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-01-28 18:27:54.271][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-01-28 18:27:54.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.290][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-01-28 18:27:54.292][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-01-28 18:27:54.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.296][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-01-28 18:27:54.298][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-01-28 18:27:54.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.303][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-01-28 18:27:54.304][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-01-28 18:27:54.308][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-01-28 18:27:54.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.313][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-01-28 18:27:54.315][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-01-28 18:27:54.316][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-01-28 18:27:54.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.321][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-01-28 18:27:54.324][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:54.325][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-01-28 18:27:54.326][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:54.328][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-01-28 18:27:54.329][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:54.330][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-01-28 18:27:54.332][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:54.333][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-01-28 18:27:54.334][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-01-28 18:27:54.336][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-01-28 18:27:54.337][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:54.338][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-01-28 18:27:54.340][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-01-28 18:27:54.341][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:54.342][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:54.344][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-01-28 18:27:54.344][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-01-28 18:27:54.344][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-01-28 18:27:54.344][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-01-28 18:27:54.344][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-01-28 18:27:54.345][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-01-28 18:27:54.346][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:27:54.348][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:27:54.349][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-01-28 18:27:54.350][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:27:54.351][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:27:54.353][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-01-28 18:27:54.354][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:54.355][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-01-28 18:27:54.356][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-01-28 18:27:54.358][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:54.359][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:54.361][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-01-28 18:27:54.363][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:54.365][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-01-28 18:27:54.366][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:54.367][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-01-28 18:27:54.369][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:54.370][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-01-28 18:27:54.371][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:54.373][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-01-28 18:27:54.374][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-01-28 18:27:54.375][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-01-28 18:27:54.377][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:54.378][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-01-28 18:27:54.379][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-01-28 18:27:54.381][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:54.382][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:54.383][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-01-28 18:27:54.383][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-01-28 18:27:54.383][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-01-28 18:27:54.383][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-01-28 18:27:54.383][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-01-28 18:27:54.385][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-01-28 18:27:54.386][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:27:54.387][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:27:54.389][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-01-28 18:27:54.390][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:27:54.391][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:27:54.393][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-01-28 18:27:54.394][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:54.395][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-01-28 18:27:54.396][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-01-28 18:27:54.398][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:54.399][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:54.401][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-01-28 18:27:54.403][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:54.405][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-01-28 18:27:54.406][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:54.408][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-01-28 18:27:54.409][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:54.410][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-01-28 18:27:54.412][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:54.413][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-01-28 18:27:54.414][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-01-28 18:27:54.416][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-01-28 18:27:54.417][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:54.419][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-01-28 18:27:54.420][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-01-28 18:27:54.421][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:54.423][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:54.424][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:54.425][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-01-28 18:27:54.427][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:27:54.428][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:27:54.429][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-01-28 18:27:54.431][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:27:54.432][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:27:54.433][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-01-28 18:27:54.435][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:54.436][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-01-28 18:27:54.437][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-01-28 18:27:54.438][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:54.440][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:54.441][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-01-28 18:27:54.444][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:54.445][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-01-28 18:27:54.446][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:54.448][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-01-28 18:27:54.449][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:54.450][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-01-28 18:27:54.452][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:54.453][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-01-28 18:27:54.455][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-01-28 18:27:54.456][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-01-28 18:27:54.457][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:54.459][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-01-28 18:27:54.460][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-01-28 18:27:54.461][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:54.463][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:54.464][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:54.465][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-01-28 18:27:54.467][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:27:54.468][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:27:54.469][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-01-28 18:27:54.471][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:27:54.472][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:27:54.473][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-01-28 18:27:54.475][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:54.476][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-01-28 18:27:54.477][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-01-28 18:27:54.478][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:54.480][self$setPropertyValue]
biodb.DEBUG[2023-01-28 18:27:54.482][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-01-28 18:27:54.483][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:54.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:54.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:54.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:54.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:54.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:54.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:54.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:54.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:54.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:54.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:54.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:54.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:54.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:54.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:54.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:54.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:54.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:54.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:54.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:54.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:54.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:54.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:54.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:54.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:54.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:54.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.563][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[2023-01-28 18:27:54.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:54.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:54.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:54.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:54.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:54.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:54.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:54.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:54.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.599][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-01-28 18:27:54.601][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-01-28 18:27:54.603][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-01-28 18:27:54.605][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-01-28 18:27:54.607][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-01-28 18:27:54.609][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-01-28 18:27:54.611][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-01-28 18:27:54.613][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-01-28 18:27:54.615][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-01-28 18:27:54.617][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-01-28 18:27:54.619][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-01-28 18:27:54.621][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-01-28 18:27:54.623][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-01-28 18:27:54.625][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-01-28 18:27:54.626][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-01-28 18:27:54.628][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-01-28 18:27:54.630][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-01-28 18:27:54.632][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-01-28 18:27:54.634][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-01-28 18:27:54.636][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-01-28 18:27:54.638][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-01-28 18:27:54.640][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-01-28 18:27:54.642][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-01-28 18:27:54.644][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-01-28 18:27:54.646][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-01-28 18:27:54.648][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-01-28 18:27:54.649][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-01-28 18:27:54.651][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-01-28 18:27:54.653][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-01-28 18:27:54.655][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-01-28 18:27:54.657][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-01-28 18:27:54.659][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-01-28 18:27:54.661][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-01-28 18:27:54.663][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-01-28 18:27:54.665][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-01-28 18:27:54.666][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-01-28 18:27:54.668][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-01-28 18:27:54.670][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-01-28 18:27:54.672][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-01-28 18:27:54.674][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-01-28 18:27:54.676][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-01-28 18:27:54.678][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-01-28 18:27:54.680][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-01-28 18:27:54.682][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-01-28 18:27:54.684][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-01-28 18:27:54.686][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-01-28 18:27:54.688][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-01-28 18:27:54.690][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-01-28 18:27:54.692][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-01-28 18:27:54.694][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-01-28 18:27:54.695][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-01-28 18:27:54.697][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-01-28 18:27:54.699][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-01-28 18:27:54.701][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-01-28 18:27:54.703][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-01-28 18:27:54.705][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-01-28 18:27:54.707][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-01-28 18:27:54.709][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-01-28 18:27:54.711][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-01-28 18:27:54.713][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-01-28 18:27:54.715][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-01-28 18:27:54.716][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-01-28 18:27:54.718][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-01-28 18:27:54.720][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-01-28 18:27:54.722][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-01-28 18:27:54.724][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-01-28 18:27:54.726][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-01-28 18:27:54.728][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-01-28 18:27:54.730][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-01-28 18:27:54.732][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-01-28 18:27:54.734][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-01-28 18:27:54.736][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-01-28 18:27:54.738][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-01-28 18:27:54.739][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-01-28 18:27:54.741][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-01-28 18:27:54.743][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-01-28 18:27:54.745][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-01-28 18:27:54.747][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-01-28 18:27:54.749][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-01-28 18:27:54.751][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-01-28 18:27:54.753][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-01-28 18:27:54.755][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-01-28 18:27:54.757][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-01-28 18:27:54.759][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-01-28 18:27:54.761][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-01-28 18:27:54.762][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-01-28 18:27:54.764][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:54.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:54.766][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:54.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:54.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:54.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:54.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:54.780][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:54.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:54.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:54.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:54.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:54.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:54.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:54.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:54.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:54.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:54.799][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:54.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:54.805][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:54.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:54.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:54.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:54.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:54.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:54.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:54.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:54.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:54.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:54.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:54.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:54.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:54.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:54.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:54.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:54.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:54.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:54.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:54.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:54.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:54.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:54.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:54.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:54.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:54.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:54.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:54.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:54.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:54.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:54.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:54.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:54.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:54.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:54.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:54.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:54.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:54.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:54.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:54.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:54.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:54.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:54.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:54.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:54.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:54.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:54.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:54.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-01-28 18:27:54.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:54.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:54.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:54.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:54.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:54.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:54.915][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-01-28 18:27:54.917][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-01-28 18:27:54.919][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:54.921][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-01-28 18:27:54.922][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:54.923][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-01-28 18:27:54.925][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:54.926][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-01-28 18:27:54.927][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:54.929][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-01-28 18:27:54.930][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-01-28 18:27:54.932][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-01-28 18:27:54.933][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:54.934][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-01-28 18:27:54.936][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-01-28 18:27:54.937][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-01-28 18:27:54.937][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-01-28 18:27:54.937][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-01-28 18:27:54.937][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-01-28 18:27:54.937][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-01-28 18:27:54.937][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-01-28 18:27:54.937][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-01-28 18:27:54.937][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-01-28 18:27:54.937][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-01-28 18:27:54.937][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-01-28 18:27:54.937][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-01-28 18:27:54.939][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-01-28 18:27:54.940][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-01-28 18:27:54.940][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-01-28 18:27:54.940][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-01-28 18:27:54.941][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-01-28 18:27:54.943][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:27:54.944][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:27:54.945][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-01-28 18:27:54.947][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-01-28 18:27:54.948][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-01-28 18:27:54.949][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-01-28 18:27:54.951][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-01-28 18:27:54.951][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-01-28 18:27:54.952][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-01-28 18:27:54.953][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-01-28 18:27:54.954][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-01-28 18:27:54.956][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-01-28 18:27:54.956][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-01-28 18:27:54.958][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-01-28 18:27:54.960][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-01-28 18:27:54.962][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-01-28 18:27:54.964][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-01-28 18:27:54.966][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-01-28 18:27:54.968][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-01-28 18:27:54.973][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-01-28 18:27:54.974][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-01-28 18:27:54.985][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-01-28 18:27:54.987][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-01-28 18:27:54.989][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-01-28 18:27:54.991][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-01-28 18:27:54.992][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-01-28 18:27:54.994][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-01-28 18:27:54.996][biodb::testThat]
biodb.INFO [2023-01-28 18:27:54.997][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2023-01-28 18:27:54.998][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-01-28 18:27:54.999][biodb::testThat]
biodb.DEBUG[2023-01-28 18:27:55.005][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-01-28 18:27:55.010][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-01-28 18:27:55.012][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2023-01-28 18:27:55.013][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-01-28 18:27:55.015][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2023-01-28 18:27:55.020][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-01-28 18:27:55.024][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-01-28 18:27:55.026][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2023-01-28 18:27:55.027][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-01-28 18:27:55.029][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2023-01-28 18:27:55.053][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2023-01-28 18:27:55.054][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-01-28 18:27:55.056][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2023-01-28 18:27:55.058][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-01-28 18:27:55.059][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-01-28 18:27:55.061][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-01-28 18:27:55.062][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-01-28 18:27:55.064][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-01-28 18:27:55.065][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-01-28 18:27:55.068][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:55.069][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:55.071][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:55.078][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:55.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:55.081][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:55.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-01-28 18:27:55.084][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2023-01-28 18:27:55.088][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-01-28 18:27:55.089][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-01-28 18:27:55.091][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2023-01-28 18:27:56.409][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2023-01-28 18:27:58.315][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-01-28 18:27:58.325][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2023-01-28 18:27:58.340][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2023-01-28 18:27:58.353][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2023-01-28 18:27:58.359][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-01-28 18:27:58.378][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-01-28 18:27:58.380][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-01-28 18:27:58.382][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-01-28 18:27:58.384][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:58.385][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:58.392][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:58.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:58.395][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:58.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-01-28 18:27:58.401][ef$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:58.402][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:58.403][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:58.405][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:58.407][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:58.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:58.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:58.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:58.416][ef$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:27:58.417][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:27:58.419][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:58.420][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:58.422][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-01-28 18:27:58.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-01-28 18:27:58.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:58.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:58.431][ef$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:27:58.433][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:27:58.434][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:58.435][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:58.437][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-01-28 18:27:58.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-01-28 18:27:58.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:58.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:58.447][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-01-28 18:27:58.448][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-01-28 18:27:58.450][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:58.451][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:58.453][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-01-28 18:27:58.455][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-01-28 18:27:58.456][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:58.457][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:58.459][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:27:58.461][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:27:58.462][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:58.463][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:58.465][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:27:58.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-01-28 18:27:58.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:58.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:58.475][ef$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:27:58.476][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:58.478][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:58.479][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:58.481][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-01-28 18:27:58.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-01-28 18:27:58.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:58.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:58.490][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:58.492][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:58.493][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:58.494][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:58.496][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:58.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-01-28 18:27:58.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:58.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:58.506][ef$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:27:58.507][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:27:58.508][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:58.510][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:58.512][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-01-28 18:27:58.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-01-28 18:27:58.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:58.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:58.521][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:27:58.523][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:27:58.524][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:58.526][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:58.528][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-01-28 18:27:58.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-01-28 18:27:58.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:58.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:58.537][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:27:58.538][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:27:58.540][ef$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:58.541][ef$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:58.543][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-01-28 18:27:58.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-01-28 18:27:58.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:58.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:58.552][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:58.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:58.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:58.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:58.558][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:58.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:58.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:58.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:58.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:58.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:58.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:58.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:58.569][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-01-28 18:27:58.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-01-28 18:27:58.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:58.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:58.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:58.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:58.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:58.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:58.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:58.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:58.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:58.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:58.601][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:58.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:58.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:58.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:58.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:58.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:58.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:58.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:58.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:58.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:58.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:58.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-01-28 18:27:58.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-01-28 18:27:58.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-01-28 18:27:58.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-01-28 18:27:58.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-01-28 18:27:58.627][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2023-01-28 18:27:58.628][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-01-28 18:27:58.630][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-01-28 18:27:58.632][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-01-28 18:27:58.633][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-01-28 18:27:58.634][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-01-28 18:27:58.635][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-01-28 18:27:58.636][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-01-28 18:27:58.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-01-28 18:27:58.639][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-01-28 18:27:58.640][FUN] Functions in observer 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 365 ]
> 
> proc.time()
   user  system elapsed 
 32.439   1.069 152.150

Example timings