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This page was generated on 2024-09-12 11:39 -0400 (Thu, 12 Sep 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4713
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4450
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4483
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4430
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4428
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 201/2258HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbChebi 1.11.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-09-11 14:00 -0400 (Wed, 11 Sep 2024)
git_url: https://git.bioconductor.org/packages/biodbChebi
git_branch: devel
git_last_commit: dfe3f6c
git_last_commit_date: 2024-04-30 11:37:31 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for biodbChebi on nebbiolo2

To the developers/maintainers of the biodbChebi package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: biodbChebi
Version: 1.11.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings biodbChebi_1.11.0.tar.gz
StartedAt: 2024-09-11 20:43:21 -0400 (Wed, 11 Sep 2024)
EndedAt: 2024-09-11 20:45:16 -0400 (Wed, 11 Sep 2024)
EllapsedTime: 115.3 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbChebi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings biodbChebi_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/biodbChebi.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.5 LTS
* using session charset: UTF-8
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.11.0’
* 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 installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

biodbChebi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL biodbChebi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-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 version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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

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

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

> # 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 [2024-09-11 20:44:04.471][biodb::testContext]
biodb.INFO [2024-09-11 20:44:04.474][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-11 20:44:04.475][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-09-11 20:44:04.476][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-11 20:44:04.477][biodb::testContext]
biodb.INFO [2024-09-11 20:44:04.484][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-09-11 20:44:04.486][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-09-11 20:44:04.495][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-11 20:44:04.496][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-09-11 20:44:04.497][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-09-11 20:44:04.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:04.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:04.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:04.501][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-09-11 20:44:04.522][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-09-11 20:44:04.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:04.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:04.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:04.526][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-09-11 20:44:04.527][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-09-11 20:44:04.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:04.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:04.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:04.531][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-09-11 20:44:04.532][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-09-11 20:44:04.533][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-09-11 20:44:04.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:04.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:04.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:04.537][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-09-11 20:44:04.538][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-09-11 20:44:04.539][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-09-11 20:44:04.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:04.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:04.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:04.542][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-09-11 20:44:04.544][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-09-11 20:44:04.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:04.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:04.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:04.547][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-09-11 20:44:04.548][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-09-11 20:44:04.549][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-09-11 20:44:04.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:04.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:04.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:04.553][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-09-11 20:44:04.554][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-09-11 20:44:04.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:04.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:04.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:04.565][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-09-11 20:44:04.566][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-09-11 20:44:04.568][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-09-11 20:44:04.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:04.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:04.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:04.571][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-09-11 20:44:04.572][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-09-11 20:44:04.574][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-09-11 20:44:04.575][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-09-11 20:44:04.576][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-09-11 20:44:04.577][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-09-11 20:44:04.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:04.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:04.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:04.581][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-09-11 20:44:04.582][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-09-11 20:44:04.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:04.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:04.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:04.585][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-09-11 20:44:04.587][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-09-11 20:44:04.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:04.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:04.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:04.590][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-09-11 20:44:04.591][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-09-11 20:44:04.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:04.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:04.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:04.595][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-09-11 20:44:04.596][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-09-11 20:44:04.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:04.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:04.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:04.600][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-09-11 20:44:04.601][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-09-11 20:44:04.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:04.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:04.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:04.605][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-09-11 20:44:04.606][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-09-11 20:44:04.610][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-09-11 20:44:04.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:04.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:04.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:04.614][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-09-11 20:44:04.615][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-09-11 20:44:04.616][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-09-11 20:44:04.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:04.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:04.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:04.624][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-09-11 20:44:04.664][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:04.703][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-09-11 20:44:04.704][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:04.705][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-11 20:44:04.706][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:04.708][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-11 20:44:04.709][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:04.710][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-11 20:44:04.711][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-09-11 20:44:04.712][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-11 20:44:04.713][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:04.714][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-09-11 20:44:04.715][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-11 20:44:04.716][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:04.717][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:04.718][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-11 20:44:04.718][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-11 20:44:04.718][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-11 20:44:04.718][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-09-11 20:44:04.718][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-09-11 20:44:04.720][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-11 20:44:04.721][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:04.722][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:04.723][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-11 20:44:04.724][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:04.724][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:04.725][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-11 20:44:04.727][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:04.728][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-11 20:44:04.728][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-11 20:44:04.729][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:04.730][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:04.732][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-09-11 20:44:04.734][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:04.735][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-09-11 20:44:04.736][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:04.737][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-11 20:44:04.738][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:04.739][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-11 20:44:04.740][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:04.741][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-11 20:44:04.742][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-09-11 20:44:04.743][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-11 20:44:04.744][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:04.745][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-09-11 20:44:04.746][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-11 20:44:04.747][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:04.748][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:04.749][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-11 20:44:04.749][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-11 20:44:04.749][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-11 20:44:04.749][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-09-11 20:44:04.749][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-09-11 20:44:04.750][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-11 20:44:04.751][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:04.752][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:04.753][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-11 20:44:04.754][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:04.755][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:04.756][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-11 20:44:04.757][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:04.758][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-11 20:44:04.759][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-11 20:44:04.760][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:04.761][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:04.762][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-09-11 20:44:04.763][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:04.764][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-09-11 20:44:04.765][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:04.766][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-11 20:44:04.767][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:04.768][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-11 20:44:04.769][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:04.770][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-11 20:44:04.771][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-09-11 20:44:04.772][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-11 20:44:04.773][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:04.774][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-09-11 20:44:04.775][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-11 20:44:04.776][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:04.777][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:04.778][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:04.779][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-11 20:44:04.780][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:04.781][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:04.782][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-11 20:44:04.783][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:04.783][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:04.784][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-11 20:44:04.785][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:04.786][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-11 20:44:04.787][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-11 20:44:04.788][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:04.789][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:04.790][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-09-11 20:44:04.792][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:04.793][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-09-11 20:44:04.794][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:04.795][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-11 20:44:04.796][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:04.797][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-11 20:44:04.798][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:04.799][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-11 20:44:04.800][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-09-11 20:44:04.801][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-11 20:44:04.802][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:04.803][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-09-11 20:44:04.804][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-11 20:44:04.804][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:04.805][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:04.806][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:04.807][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-11 20:44:04.808][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:04.809][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:04.810][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-11 20:44:04.811][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:04.812][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:04.813][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-11 20:44:04.814][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:04.815][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-11 20:44:04.815][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-11 20:44:04.816][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:04.817][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:04.822][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-11 20:44:04.822][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:04.823][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.DEBUG[2024-09-11 20:44:04.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:04.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:04.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:04.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:04.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:04.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:04.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:04.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:04.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:04.832][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[2024-09-11 20:44:04.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:04.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:04.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:04.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:04.836][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[2024-09-11 20:44:04.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:04.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:04.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:04.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:04.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:04.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:04.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:04.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:04.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:04.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:04.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:04.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:04.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:04.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:04.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:04.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:04.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:04.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:04.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:04.853][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[2024-09-11 20:44:04.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:04.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:04.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:04.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:04.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:04.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:04.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:04.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:04.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:04.861][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[2024-09-11 20:44:04.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:04.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:04.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:04.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:04.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:04.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:04.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:04.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:04.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:04.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:04.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:04.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:04.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:04.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:04.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:04.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:04.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:04.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:04.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:04.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:04.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:04.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:04.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:04.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:04.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:04.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:04.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:04.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:04.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:04.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:04.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:04.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:04.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:04.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:04.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:04.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:04.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:04.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:04.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:04.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:04.894][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-09-11 20:44:04.899][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-09-11 20:44:04.900][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-09-11 20:44:04.901][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-09-11 20:44:04.903][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-09-11 20:44:04.904][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-09-11 20:44:04.905][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-09-11 20:44:04.906][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-09-11 20:44:04.908][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-09-11 20:44:04.909][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-09-11 20:44:04.910][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-09-11 20:44:04.911][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-09-11 20:44:04.913][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-09-11 20:44:04.914][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-09-11 20:44:04.915][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-09-11 20:44:04.916][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-09-11 20:44:04.918][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-09-11 20:44:04.919][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-09-11 20:44:04.920][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-09-11 20:44:04.921][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-09-11 20:44:04.923][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-09-11 20:44:04.924][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-09-11 20:44:04.925][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-09-11 20:44:04.926][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-09-11 20:44:04.928][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-09-11 20:44:04.929][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-09-11 20:44:04.930][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-09-11 20:44:04.932][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-09-11 20:44:04.933][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-09-11 20:44:04.934][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-09-11 20:44:04.935][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-09-11 20:44:04.937][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-09-11 20:44:04.938][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-09-11 20:44:04.939][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-09-11 20:44:04.941][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-09-11 20:44:04.942][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-09-11 20:44:04.948][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-09-11 20:44:04.949][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-09-11 20:44:04.950][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-09-11 20:44:04.952][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-09-11 20:44:04.953][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-09-11 20:44:04.954][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-09-11 20:44:04.955][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-09-11 20:44:04.957][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-09-11 20:44:04.958][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-09-11 20:44:04.959][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-09-11 20:44:04.960][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-09-11 20:44:04.962][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-09-11 20:44:04.963][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-09-11 20:44:04.964][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-09-11 20:44:04.965][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-09-11 20:44:04.966][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-09-11 20:44:04.968][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-09-11 20:44:04.969][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-09-11 20:44:04.970][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-09-11 20:44:04.971][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-09-11 20:44:04.973][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-09-11 20:44:04.974][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-09-11 20:44:04.975][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-09-11 20:44:04.977][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-09-11 20:44:04.978][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-09-11 20:44:04.979][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-09-11 20:44:04.980][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-09-11 20:44:04.982][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-09-11 20:44:04.983][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-09-11 20:44:04.984][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-09-11 20:44:04.985][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-09-11 20:44:04.987][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-09-11 20:44:04.988][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-09-11 20:44:04.989][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-09-11 20:44:04.990][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-09-11 20:44:04.992][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-09-11 20:44:04.993][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-09-11 20:44:04.994][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-09-11 20:44:04.995][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-09-11 20:44:04.997][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-09-11 20:44:04.998][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-09-11 20:44:04.999][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-09-11 20:44:05.001][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-09-11 20:44:05.002][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-09-11 20:44:05.003][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-09-11 20:44:05.004][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-09-11 20:44:05.006][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-09-11 20:44:05.011][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-09-11 20:44:05.013][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-09-11 20:44:05.016][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-11 20:44:05.017][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:05.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:05.018][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:05.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:05.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:05.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:05.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:05.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:05.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:05.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:05.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:05.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:05.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:05.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:05.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:05.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:05.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:05.034][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[2024-09-11 20:44:05.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:05.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:05.037][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:05.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:05.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:05.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:05.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:05.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:05.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:05.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:05.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:05.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:05.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:05.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:05.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:05.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:05.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:05.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:05.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:05.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:05.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:05.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:05.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:05.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:05.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:05.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:05.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:05.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:05.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:05.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:05.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:05.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:05.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:05.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:05.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:05.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:05.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:05.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:05.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:05.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:05.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:05.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:05.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:05.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:05.070][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:05.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:05.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:05.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:05.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:05.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:05.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:05.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:05.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:05.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:05.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:05.079][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[2024-09-11 20:44:05.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:05.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:05.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:05.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:05.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:05.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:05.085][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[2024-09-11 20:44:05.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:05.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:05.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:05.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:05.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:05.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:05.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:05.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:05.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:05.093][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:05.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:05.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:05.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:05.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:05.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:05.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:05.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:05.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:05.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:05.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:05.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:05.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:05.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:05.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:05.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:05.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:05.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:05.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:05.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:05.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:05.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:05.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:05.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:05.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:05.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:05.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:05.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:05.115][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:05.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:05.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:05.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:05.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:05.120][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-09-11 20:44:05.129][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-09-11 20:44:05.130][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:05.131][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-09-11 20:44:05.132][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:05.133][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-11 20:44:05.134][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:05.135][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-11 20:44:05.136][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:05.137][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-09-11 20:44:05.138][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-09-11 20:44:05.139][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-11 20:44:05.140][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:05.140][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-09-11 20:44:05.141][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-11 20:44:05.142][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-09-11 20:44:05.142][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-09-11 20:44:05.142][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-09-11 20:44:05.142][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-09-11 20:44:05.142][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-09-11 20:44:05.142][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-09-11 20:44:05.142][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-09-11 20:44:05.142][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-09-11 20:44:05.142][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-09-11 20:44:05.142][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-09-11 20:44:05.142][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-09-11 20:44:05.143][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:05.144][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-11 20:44:05.144][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-11 20:44:05.144][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-11 20:44:05.145][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-09-11 20:44:05.146][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:05.147][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:05.148][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-11 20:44:05.149][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:05.149][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:05.150][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-11 20:44:05.151][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-11 20:44:05.151][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-09-11 20:44:05.152][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-11 20:44:05.153][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-11 20:44:05.154][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:05.155][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-09-11 20:44:05.155][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-09-11 20:44:05.160][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-09-11 20:44:05.162][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-09-11 20:44:05.163][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-09-11 20:44:05.164][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-09-11 20:44:05.166][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-09-11 20:44:05.167][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-09-11 20:44:05.196][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-09-11 20:44:05.197][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-09-11 20:44:05.201][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-09-11 20:44:05.205][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-09-11 20:44:05.210][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-11 20:44:05.211][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-11 20:44:05.212][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-09-11 20:44:05.213][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-09-11 20:44:05.222][biodb::testThat]
biodb.INFO [2024-09-11 20:44:05.223][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-09-11 20:44:05.224][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-11 20:44:05.225][biodb::testThat]
biodb.TRACE[2024-09-11 20:44:05.229][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2024-09-11 20:44:05.231][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-11 20:44:05.234][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-11 20:44:05.243][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:05.244][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:05.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:05.257][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:05.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:05.259][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:05.260][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[2024-09-11 20:44:05.270][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:05.271][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:05.272][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.273][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:05.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:05.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.289][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:05.290][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:05.291][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.292][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.317][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:05.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:05.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.321][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:05.322][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:05.323][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.324][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.325][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:05.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:05.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.329][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:05.330][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:05.331][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.332][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.333][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:05.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:05.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.337][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:05.338][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:05.339][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.340][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.341][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:05.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:05.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.345][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:05.345][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:05.346][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.347][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.348][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:05.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:05.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.352][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:05.353][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:05.354][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.355][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.356][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:05.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:05.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.360][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:05.361][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:05.362][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.362][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.364][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:05.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:05.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.367][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:05.368][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:05.369][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.370][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.371][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:05.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:05.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.375][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:05.376][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:05.377][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.378][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.379][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:05.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:05.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.383][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:05.384][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:05.385][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.386][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.387][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:05.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:05.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.391][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:05.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:05.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.395][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:05.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:05.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:05.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:05.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.402][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:05.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:05.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:05.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:05.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:05.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:05.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:05.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:05.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:05.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:05.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.464][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:05.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:05.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.468][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:05.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:05.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:05.472][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-09-11 20:44:05.474][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:05.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:05.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.478][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:05.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:05.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.503][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:05.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:05.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.508][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:05.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:05.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.511][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:05.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:05.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.515][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:05.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:05.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.519][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-11 20:44:05.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-11 20:44:05.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.522][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-11 20:44:05.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-11 20:44:05.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.526][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-09-11 20:44:05.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-09-11 20:44:05.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.530][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-09-11 20:44:05.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-09-11 20:44:05.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:05.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:05.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.565][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:05.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:05.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:05.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:05.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:05.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:05.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:05.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:05.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:05.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:05.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:05.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:05.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:05.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:05.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.596][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:05.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:05.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:05.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:05.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.604][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:05.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:05.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:05.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:05.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:05.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:05.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.623][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:05.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:05.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.627][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:05.628][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:05.629][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.630][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:05.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:05.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.643][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:05.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:05.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.679][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:05.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:05.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.683][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:05.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:05.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.687][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:05.688][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:05.689][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.690][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.690][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:05.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:05.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.701][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:05.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:05.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.705][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:05.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:05.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.709][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:05.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:05.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.713][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:05.714][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:05.715][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.716][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.717][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:05.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:05.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.729][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:05.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:05.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.733][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:05.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:05.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.736][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:05.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:05.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.740][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:05.741][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:05.742][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.743][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.744][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:05.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:05.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.755][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:05.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:05.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.759][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:05.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:05.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.762][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:05.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:05.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.766][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:05.767][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:05.768][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.769][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.770][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:05.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:05.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.781][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:05.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:05.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.785][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:05.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:05.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.789][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:05.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:05.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.792][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:05.793][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:05.794][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.795][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.796][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:05.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:05.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.808][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:05.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:05.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.812][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:05.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:05.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.816][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:05.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:05.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.820][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:05.821][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:05.822][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.823][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.824][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:05.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:05.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.835][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-09-11 20:44:05.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:05.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.839][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-09-11 20:44:05.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:05.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.842][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-09-11 20:44:05.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:05.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.846][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-09-11 20:44:05.847][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:05.848][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.849][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.850][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-09-11 20:44:05.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:05.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.861][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:05.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:05.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.865][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:05.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:05.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.869][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:05.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:05.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.873][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:05.874][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:05.875][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.875][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.876][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:05.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:05.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.888][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:05.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:05.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.892][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:05.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:05.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.904][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:05.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:05.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.908][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:05.909][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:05.910][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.911][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.912][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:05.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:05.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.924][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:05.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:05.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.929][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:05.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:05.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.933][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:05.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:05.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.937][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:05.938][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:05.938][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.939][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.940][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:05.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:05.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.952][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:05.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:05.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.956][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:05.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:05.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.960][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:05.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:05.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.964][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:05.965][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:05.965][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.966][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.967][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:05.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:05.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.978][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:05.979][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:05.980][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.981][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.985][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:05.986][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:05.987][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.988][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:05.992][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:05.993][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:05.994][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:05.995][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.000][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:06.001][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:06.002][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.003][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.008][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:06.009][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:06.010][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.011][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.015][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:06.016][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:06.017][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.018][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.022][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:06.023][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:06.024][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.024][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.028][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:06.029][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:06.030][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.031][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.035][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-09-11 20:44:06.036][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:06.037][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.038][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.042][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:06.043][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:06.044][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.045][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.049][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:06.050][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:06.051][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.051][ef$get] fields variable is a list.
biodb.INFO [2024-09-11 20:44:06.058][biodb::testThat]
biodb.INFO [2024-09-11 20:44:06.059][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-09-11 20:44:06.060][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-11 20:44:06.061][biodb::testThat]
biodb.DEBUG[2024-09-11 20:44:06.074][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-09-11 20:44:06.082][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-11 20:44:06.087][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-09-11 20:44:06.088][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-11 20:44:06.090][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-09-11 20:44:06.091][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-11 20:44:06.113][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-11 20:44:06.120][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-11 20:44:06.122][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:06.123][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:06.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:06.128][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:06.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:06.130][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:06.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:06.133][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:06.134][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:06.135][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.136][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:06.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:06.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.158][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:06.159][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:06.160][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.161][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.162][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:06.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:06.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.166][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:06.167][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:06.168][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.168][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.170][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:06.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:06.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.174][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:06.175][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:06.175][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.176][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.178][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:06.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:06.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.181][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:06.182][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:06.183][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.184][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.186][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:06.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:06.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.189][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:06.190][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:06.191][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.192][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.194][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:06.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:06.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.197][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:06.198][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:06.199][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.200][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.201][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:06.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:06.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.205][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:06.206][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:06.207][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.208][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.209][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:06.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:06.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.213][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:06.214][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:06.215][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.216][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.218][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:06.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:06.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.221][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:06.222][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:06.223][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.224][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.225][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:06.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:06.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.229][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:06.230][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:06.231][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.232][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.233][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:06.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:06.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.237][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:06.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:06.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.240][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:06.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:06.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:06.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:06.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.248][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:06.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:06.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:06.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:06.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:06.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:06.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:06.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:06.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:06.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:06.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:06.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:06.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:06.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:06.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:06.274][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-09-11 20:44:06.275][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-09-11 20:44:06.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-09-11 20:44:06.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.278][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-09-11 20:44:06.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-09-11 20:44:06.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.282][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-09-11 20:44:06.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-09-11 20:44:06.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-09-11 20:44:06.293][biodb::testThat]
biodb.INFO [2024-09-11 20:44:06.294][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-09-11 20:44:06.294][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-11 20:44:06.295][biodb::testThat]
biodb.TRACE[2024-09-11 20:44:06.298][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:06.299][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:06.300][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.301][ef$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:06.302][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-09-11 20:44:06.332][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:06.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:06.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.337][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:06.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:06.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.340][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:06.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:06.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:06.347][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-09-11 20:44:06.351][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-09-11 20:44:06.371][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-11 20:44:06.387][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-09-11 20:44:06.388][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-11 20:44:06.389][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-09-11 20:44:06.411][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[2024-09-11 20:44:06.414][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-11 20:44:06.416][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-09-11 20:44:06.417][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-11 20:44:06.418][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-09-11 20:44:06.420][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-09-11 20:44:06.430][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:06.431][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:06.432][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.433][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.434][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:06.435][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:06.436][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.437][ef$get] fields variable is a list.
biodb.INFO [2024-09-11 20:44:06.441][biodb::testThat]
biodb.INFO [2024-09-11 20:44:06.442][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-09-11 20:44:06.443][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-11 20:44:06.443][biodb::testThat]
biodb.TRACE[2024-09-11 20:44:06.466][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:06.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:06.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.470][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:06.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:06.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.474][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:06.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:06.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:06.537][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[2024-09-11 20:44:06.540][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-11 20:44:06.541][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-09-11 20:44:06.543][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-11 20:44:06.544][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-09-11 20:44:06.558][biodb::testThat]
biodb.INFO [2024-09-11 20:44:06.559][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-09-11 20:44:06.560][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-11 20:44:06.561][biodb::testThat]
biodb.TRACE[2024-09-11 20:44:06.578][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:06.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:06.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.582][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:06.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:06.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.586][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:06.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:06.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.590][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:06.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:06.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.593][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:06.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:06.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.597][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:06.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:06.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.601][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-11 20:44:06.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-11 20:44:06.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.604][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-11 20:44:06.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-11 20:44:06.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.608][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-09-11 20:44:06.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-09-11 20:44:06.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.611][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-09-11 20:44:06.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-09-11 20:44:06.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.631][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:06.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:06.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.635][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:06.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:06.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.639][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:06.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:06.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.643][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:06.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:06.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.646][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:06.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:06.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.650][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:06.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:06.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.653][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-11 20:44:06.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-11 20:44:06.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.657][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-11 20:44:06.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-11 20:44:06.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.661][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-09-11 20:44:06.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-09-11 20:44:06.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:06.664][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-09-11 20:44:06.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-09-11 20:44:06.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:06.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-09-11 20:44:06.673][biodb::testThat]
biodb.INFO [2024-09-11 20:44:06.673][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-09-11 20:44:06.674][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-11 20:44:06.675][biodb::testThat]
biodb.INFO [2024-09-11 20:44:06.682][biodb::testThat]
biodb.INFO [2024-09-11 20:44:06.683][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-09-11 20:44:06.684][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-11 20:44:06.685][biodb::testThat]
biodb.INFO [2024-09-11 20:44:06.693][biodb::testThat]
biodb.INFO [2024-09-11 20:44:06.693][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-09-11 20:44:06.694][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-11 20:44:06.695][biodb::testThat]
biodb.DEBUG[2024-09-11 20:44:06.699][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-09-11 20:44:07.358][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-09-11 20:44:08.480][biodb::testThat]
biodb.INFO [2024-09-11 20:44:08.481][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-09-11 20:44:08.482][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-11 20:44:08.483][biodb::testThat]
biodb.DEBUG[2024-09-11 20:44:08.897][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[2024-09-11 20:44:09.314][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:09.315][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:09.316][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:09.317][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:09.318][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:09.319][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:09.320][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:09.321][ef$get] fields variable is a list.
biodb.INFO [2024-09-11 20:44:09.323][biodb::testThat]
biodb.INFO [2024-09-11 20:44:09.324][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-09-11 20:44:09.325][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-11 20:44:09.326][biodb::testThat]
biodb.TRACE[2024-09-11 20:44:09.335][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:09.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:09.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:09.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:09.339][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:09.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:09.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:09.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:09.343][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:09.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:09.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:09.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:09.435][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[2024-09-11 20:44:09.438][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-11 20:44:09.439][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-09-11 20:44:09.441][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-11 20:44:09.442][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-09-11 20:44:09.498][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[2024-09-11 20:44:09.501][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-11 20:44:09.502][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-09-11 20:44:09.504][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-11 20:44:09.505][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-09-11 20:44:09.517][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-11 20:44:09.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-11 20:44:09.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:09.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:09.524][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:09.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:09.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:09.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:09.528][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:09.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:09.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:09.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:09.532][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:09.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:09.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:09.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:09.535][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:09.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:09.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:09.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:09.539][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:09.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:09.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:09.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:09.549][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[2024-09-11 20:44:09.552][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-11 20:44:09.554][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-09-11 20:44:09.555][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-11 20:44:09.556][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-09-11 20:44:09.558][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:09.559][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:09.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:09.564][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:09.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:09.566][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:09.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:09.567][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-09-11 20:44:09.618][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-11 20:44:09.619][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-09-11 20:44:09.621][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-11 20:44:09.622][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-11 20:44:09.623][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-11 20:44:09.624][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-11 20:44:09.624][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-11 20:44:09.625][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-11 20:44:09.628][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:09.629][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:09.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:09.634][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:09.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:09.635][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:09.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:09.637][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-09-11 20:44:09.640][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-11 20:44:09.641][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-11 20:44:09.642][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-09-11 20:44:10.044][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-09-11 20:44:10.438][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-11 20:44:10.440][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-09-11 20:44:10.454][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-09-11 20:44:10.457][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-09-11 20:44:10.458][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-11 20:44:10.459][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-11 20:44:10.461][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-11 20:44:10.462][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:10.463][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:10.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:10.468][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:10.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:10.470][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:10.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:10.473][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:10.474][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:10.475][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:10.476][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:10.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:10.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:10.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:10.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:10.481][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:10.482][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:10.483][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:10.484][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:10.485][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:10.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:10.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:10.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:10.489][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:10.490][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:10.491][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:10.492][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:10.493][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:10.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:10.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:10.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:10.497][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:10.498][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:10.499][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:10.500][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:10.501][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:10.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:10.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:10.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:10.504][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:10.505][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:10.506][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:10.507][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:10.508][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:10.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:10.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:10.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:10.512][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:10.513][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:10.514][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:10.515][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:10.516][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:10.517][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:10.518][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:10.518][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:10.527][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:10.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:10.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:10.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:10.531][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:10.532][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:10.533][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:10.533][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:10.535][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:10.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:10.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:10.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:10.538][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:10.539][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:10.540][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:10.541][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:10.542][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:10.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:10.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:10.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:10.546][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:10.547][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:10.548][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:10.549][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:10.550][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:10.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:10.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:10.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:10.554][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:10.555][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:10.556][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:10.556][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:10.558][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:10.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:10.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:10.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:10.561][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:10.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:10.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:10.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:10.565][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:10.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:10.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:10.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:10.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:10.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:10.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:10.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:10.572][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:10.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:10.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:10.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:10.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:10.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:10.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:10.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:10.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:10.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:10.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:10.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:10.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:10.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:10.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:10.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:10.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:10.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:10.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:10.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:10.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:10.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:10.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:10.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:10.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:10.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:10.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:10.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:10.598][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-09-11 20:44:10.607][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:10.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:10.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:10.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:10.611][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:10.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:10.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:10.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:10.615][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:10.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:10.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:10.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:10.619][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[2024-09-11 20:44:10.622][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-11 20:44:10.624][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-09-11 20:44:10.625][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-11 20:44:10.626][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-09-11 20:44:10.641][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:10.642][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:10.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:10.647][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:10.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:10.649][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:10.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:10.651][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:10.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:10.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:10.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:10.654][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:10.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:10.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:10.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:10.658][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:10.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:10.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:10.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:10.662][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:10.663][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:10.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:10.668][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:10.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:10.669][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:10.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:10.671][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-09-11 20:44:10.672][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-11 20:44:10.674][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-09-11 20:44:10.675][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-11 20:44:10.676][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-11 20:44:10.677][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-11 20:44:10.678][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-11 20:44:10.679][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-11 20:44:10.680][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-11 20:44:10.698][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:10.699][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:10.700][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:10.705][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:10.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:10.707][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:10.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:10.709][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-09-11 20:44:10.724][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-11 20:44:10.725][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-11 20:44:10.739][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-09-11 20:44:11.124][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-09-11 20:44:11.515][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-11 20:44:11.520][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-09-11 20:44:11.527][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-09-11 20:44:11.532][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-09-11 20:44:11.535][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-11 20:44:11.538][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-11 20:44:11.541][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-11 20:44:11.544][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:11.546][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:11.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:11.557][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:11.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:11.561][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:11.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:11.566][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:11.568][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:11.569][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:11.571][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:11.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:11.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:11.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:11.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:11.579][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:11.580][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:11.581][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:11.583][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:11.584][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:11.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:11.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:11.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:11.589][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:11.591][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:11.592][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:11.593][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:11.594][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:11.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:11.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:11.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:11.599][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:11.600][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:11.601][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:11.602][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:11.603][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:11.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:11.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:11.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:11.607][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:11.608][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:11.609][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:11.610][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:11.611][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:11.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:11.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:11.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:11.615][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:11.616][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:11.617][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:11.617][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:11.619][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:11.620][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:11.621][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:11.621][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:11.623][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:11.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:11.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:11.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:11.626][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:11.627][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:11.628][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:11.629][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:11.630][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:11.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:11.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:11.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:11.634][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:11.635][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:11.636][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:11.637][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:11.638][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:11.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:11.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:11.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:11.642][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:11.643][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:11.644][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:11.645][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:11.646][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:11.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:11.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:11.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:11.650][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:11.651][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:11.652][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:11.653][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:11.659][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:11.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:11.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:11.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:11.666][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:11.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:11.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:11.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:11.669][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:11.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:11.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:11.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:11.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:11.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:11.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:11.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:11.677][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:11.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:11.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:11.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:11.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:11.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:11.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:11.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:11.684][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:11.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:11.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:11.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:11.688][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:11.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:11.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:11.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:11.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:11.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:11.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:11.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:11.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:11.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:11.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:11.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:11.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:11.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:11.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:11.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:11.702][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-09-11 20:44:11.703][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:11.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:11.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:11.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:11.707][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:11.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:11.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:11.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:11.711][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:11.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:11.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:11.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:11.730][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[2024-09-11 20:44:11.733][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-11 20:44:11.734][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-09-11 20:44:11.736][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-11 20:44:11.737][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-09-11 20:44:11.740][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:11.741][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:11.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:11.746][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:11.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:11.747][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:11.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:11.749][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:11.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:11.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:11.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:11.753][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:11.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:11.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:11.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:11.757][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:11.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:11.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:11.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:11.760][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:11.761][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:11.762][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:11.766][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:11.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:11.768][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:11.769][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.DEBUG[2024-09-11 20:44:11.770][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-09-11 20:44:11.771][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-11 20:44:11.772][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-09-11 20:44:11.773][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-11 20:44:11.774][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-11 20:44:11.775][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-11 20:44:11.776][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-11 20:44:11.777][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-11 20:44:11.778][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-11 20:44:11.781][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:11.782][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:11.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:11.787][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:11.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:11.788][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:11.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:11.790][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-09-11 20:44:11.793][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-11 20:44:11.794][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-11 20:44:11.795][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-09-11 20:44:12.180][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-09-11 20:44:12.612][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-11 20:44:12.616][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-09-11 20:44:12.624][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-09-11 20:44:12.629][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-09-11 20:44:12.632][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-11 20:44:12.635][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-11 20:44:12.637][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-11 20:44:12.641][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:12.643][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:12.645][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:12.654][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:12.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:12.657][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:12.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:12.663][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:12.665][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:12.666][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:12.668][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:12.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:12.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:12.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:12.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:12.685][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:12.686][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:12.687][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:12.688][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:12.690][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:12.691][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:12.692][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:12.693][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:12.695][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:12.696][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:12.697][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:12.698][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:12.699][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:12.700][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:12.701][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:12.702][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:12.704][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:12.705][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:12.706][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:12.706][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:12.708][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:12.709][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:12.710][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:12.711][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:12.712][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:12.713][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:12.714][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:12.715][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:12.716][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:12.717][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:12.718][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:12.719][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:12.721][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:12.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:12.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:12.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:12.724][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:12.725][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:12.726][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:12.727][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:12.729][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:12.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:12.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:12.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:12.733][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:12.733][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:12.734][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:12.735][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:12.737][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:12.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:12.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:12.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:12.740][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:12.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:12.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:12.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:12.744][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:12.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:12.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:12.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:12.748][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:12.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:12.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:12.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:12.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:12.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:12.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:12.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:12.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:12.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:12.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:12.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:12.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:12.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:12.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:12.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:12.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:12.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:12.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:12.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:12.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:12.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:12.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:12.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:12.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:12.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:12.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:12.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:12.782][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-09-11 20:44:12.783][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:12.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:12.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:12.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:12.787][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:12.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:12.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:12.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:12.791][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:12.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:12.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:12.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:12.795][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:12.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:12.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:12.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:12.800][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:12.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:12.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:12.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:12.805][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:12.806][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:12.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:12.813][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:12.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:12.814][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:12.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:12.817][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-09-11 20:44:12.818][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-11 20:44:12.820][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-09-11 20:44:12.821][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-11 20:44:12.822][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-11 20:44:12.823][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-11 20:44:12.824][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-11 20:44:12.825][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-11 20:44:12.826][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-11 20:44:12.829][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:12.830][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:12.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:12.836][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:12.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:12.838][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:12.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:12.840][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-09-11 20:44:12.843][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-11 20:44:12.844][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-11 20:44:12.845][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-09-11 20:44:13.230][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-09-11 20:44:13.656][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-11 20:44:13.660][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-09-11 20:44:13.665][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-09-11 20:44:13.669][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-09-11 20:44:13.671][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-11 20:44:13.673][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-11 20:44:13.675][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-11 20:44:13.678][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:13.679][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:13.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:13.705][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:13.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:13.713][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:13.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:13.718][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:13.719][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:13.721][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:13.722][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:13.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:13.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:13.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:13.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:13.730][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:13.732][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:13.733][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:13.735][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:13.737][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:13.739][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:13.740][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:13.742][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:13.744][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:13.746][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:13.747][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:13.749][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:13.751][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:13.752][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:13.754][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:13.755][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:13.758][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:13.759][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:13.761][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:13.762][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:13.764][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:13.766][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:13.768][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:13.769][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:13.771][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:13.773][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:13.774][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:13.776][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:13.778][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:13.779][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:13.781][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:13.782][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:13.785][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:13.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:13.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:13.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:13.791][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:13.793][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:13.794][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:13.796][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:13.798][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:13.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:13.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:13.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:13.804][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:13.806][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:13.807][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:13.809][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:13.811][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:13.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:13.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:13.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:13.818][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:13.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:13.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:13.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:13.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:13.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:13.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:13.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:13.826][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:13.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:13.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:13.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:13.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:13.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:13.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:13.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:13.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:13.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:13.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:13.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:13.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:13.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:13.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:13.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:13.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:13.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:13.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:13.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:13.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:13.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:13.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:13.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:13.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:13.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:13.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:13.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:13.852][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-09-11 20:44:13.853][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:13.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:13.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:13.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:13.856][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:13.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:13.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:13.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:13.860][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:13.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:13.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:13.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:13.864][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:13.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:13.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:13.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:13.867][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:13.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:13.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:13.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:13.871][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:13.872][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:13.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:13.877][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:13.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:13.879][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:13.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:13.881][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-09-11 20:44:13.882][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-11 20:44:13.883][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-09-11 20:44:13.884][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-11 20:44:13.885][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-11 20:44:13.886][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-11 20:44:13.887][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-11 20:44:13.888][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-11 20:44:13.889][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-11 20:44:13.892][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:13.892][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:13.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:13.898][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:13.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:13.899][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:13.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:13.901][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-09-11 20:44:13.904][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-11 20:44:13.905][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-11 20:44:13.906][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-09-11 20:44:14.294][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-09-11 20:44:14.713][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-11 20:44:14.716][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-09-11 20:44:14.723][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-09-11 20:44:14.729][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-09-11 20:44:14.745][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-11 20:44:14.748][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-11 20:44:14.750][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-11 20:44:14.753][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:14.755][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:14.757][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:14.765][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:14.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:14.768][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:14.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:14.772][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:14.774][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:14.775][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:14.776][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:14.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:14.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:14.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:14.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:14.783][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:14.785][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:14.786][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:14.787][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:14.788][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:14.790][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:14.791][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:14.792][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:14.793][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:14.794][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:14.795][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:14.796][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:14.798][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:14.799][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:14.800][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:14.800][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:14.802][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:14.803][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:14.804][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:14.804][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:14.806][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:14.807][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:14.807][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:14.808][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:14.810][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:14.810][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:14.811][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:14.812][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:14.813][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:14.814][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:14.815][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:14.816][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:14.818][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:14.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:14.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:14.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:14.822][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:14.823][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:14.824][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:14.825][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:14.826][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:14.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:14.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:14.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:14.829][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:14.830][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:14.831][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:14.832][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:14.833][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:14.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:14.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:14.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:14.837][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:14.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:14.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:14.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:14.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:14.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:14.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:14.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:14.845][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:14.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:14.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:14.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:14.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:14.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:14.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:14.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:14.852][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:14.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:14.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:14.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:14.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:14.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:14.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:14.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:14.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:14.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:14.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:14.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:14.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:14.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:14.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:14.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:14.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:14.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:14.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:14.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:14.872][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-09-11 20:44:14.873][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:14.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:14.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:14.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:14.876][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:14.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:14.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:14.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:14.880][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:14.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:14.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:14.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:14.884][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:14.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:14.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:14.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:14.888][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:14.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:14.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:14.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:14.891][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:14.892][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:14.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:14.897][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:14.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:14.899][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:14.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:14.901][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-09-11 20:44:14.902][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-11 20:44:14.904][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-09-11 20:44:14.905][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-11 20:44:14.906][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-11 20:44:14.907][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-11 20:44:14.908][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-11 20:44:14.909][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-11 20:44:14.910][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-11 20:44:14.912][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:14.913][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:14.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:14.918][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:14.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:14.920][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:14.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:14.922][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-09-11 20:44:14.925][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-11 20:44:14.926][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-11 20:44:14.932][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-09-11 20:44:15.320][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-09-11 20:44:15.749][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-11 20:44:15.753][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-09-11 20:44:15.760][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-09-11 20:44:15.766][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-09-11 20:44:15.769][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-11 20:44:15.772][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-11 20:44:15.774][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-11 20:44:15.778][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:15.780][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:15.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:15.791][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:15.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:15.794][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:15.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:15.800][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:15.802][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:15.803][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:15.805][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:15.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:15.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:15.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:15.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:15.812][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:15.814][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:15.815][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:15.816][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:15.818][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:15.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:15.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:15.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:15.823][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:15.824][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:15.825][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:15.826][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:15.828][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:15.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:15.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:15.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:15.832][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:15.833][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:15.834][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:15.835][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:15.836][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:15.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:15.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:15.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:15.840][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:15.841][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:15.842][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:15.843][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:15.844][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:15.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:15.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:15.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:15.848][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:15.849][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:15.850][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:15.851][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:15.852][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:15.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:15.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:15.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:15.856][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:15.857][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:15.857][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:15.858][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:15.859][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:15.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:15.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:15.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:15.863][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:15.864][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:15.865][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:15.866][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:15.867][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:15.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:15.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:15.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:15.871][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:15.872][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:15.873][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:15.874][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:15.875][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:15.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:15.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:15.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:15.879][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:15.880][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:15.881][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:15.881][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:15.883][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:15.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:15.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:15.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:15.886][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:15.887][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:15.888][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:15.889][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:15.890][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:15.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:15.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:15.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:15.894][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:15.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:15.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:15.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:15.898][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:15.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:15.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:15.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:15.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:15.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:15.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:15.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:15.905][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:15.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:15.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:15.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:15.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:15.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:15.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:15.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:15.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:15.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:15.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:15.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:15.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:15.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:15.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:15.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:15.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:15.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:15.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:15.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:15.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:15.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:15.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:15.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:15.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:15.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:15.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:15.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:15.930][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-09-11 20:44:15.931][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:15.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:15.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:15.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:15.935][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:15.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:15.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:15.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:15.939][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:15.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:15.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:15.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:15.942][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:15.951][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:15.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:15.956][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:15.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:15.958][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:15.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:15.959][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-09-11 20:44:15.960][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-11 20:44:15.962][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-09-11 20:44:15.963][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-11 20:44:15.964][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-11 20:44:15.965][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-11 20:44:15.966][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-11 20:44:15.967][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-11 20:44:15.968][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-11 20:44:15.971][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:15.971][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:15.972][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:15.977][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:15.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:15.978][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:15.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:15.980][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-09-11 20:44:15.983][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-11 20:44:15.984][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-11 20:44:15.985][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-09-11 20:44:16.372][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-09-11 20:44:16.801][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-11 20:44:16.806][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-09-11 20:44:16.814][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-09-11 20:44:16.819][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-09-11 20:44:16.822][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-11 20:44:16.825][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-11 20:44:16.828][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-11 20:44:16.831][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:16.833][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:16.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:16.844][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:16.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:16.848][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:16.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:16.854][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:16.856][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:16.857][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:16.859][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:16.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:16.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:16.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:16.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:16.866][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:16.868][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:16.869][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:16.871][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:16.872][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:16.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:16.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:16.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:16.877][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:16.878][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:16.879][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:16.880][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:16.882][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:16.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:16.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:16.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:16.887][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:16.888][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:16.889][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:16.890][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:16.891][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:16.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:16.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:16.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:16.895][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:16.896][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:16.897][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:16.898][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:16.899][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:16.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:16.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:16.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:16.902][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:16.903][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:16.904][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:16.905][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:16.906][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:16.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:16.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:16.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:16.910][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:16.911][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:16.912][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:16.913][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:16.914][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:16.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:16.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:16.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:16.918][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:16.919][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:16.919][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:16.920][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:16.921][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:16.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:16.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:16.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:16.925][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:16.926][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:16.927][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:16.928][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:16.929][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:16.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:16.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:16.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:16.933][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:16.934][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:16.935][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:16.936][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:16.937][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:16.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:16.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:16.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:16.940][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:16.941][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:16.942][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:16.943][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:16.944][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:16.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:16.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:16.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:16.948][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:16.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:16.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:16.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:16.952][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:16.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:16.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:16.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:16.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:16.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:16.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:16.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:16.959][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:16.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:16.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:16.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:16.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:16.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:16.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:16.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:16.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:16.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:16.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:16.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:16.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:16.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:16.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:16.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:16.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:16.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:16.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:16.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:16.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:16.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:16.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:16.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:16.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:16.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:16.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:16.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:16.993][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-09-11 20:44:16.994][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:16.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:16.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:16.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:16.997][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:16.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:16.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:17.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:17.001][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:17.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:17.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:17.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:17.005][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:17.005][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:17.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:17.011][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:17.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:17.012][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:17.013][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[2024-09-11 20:44:17.014][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-09-11 20:44:17.015][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-11 20:44:17.017][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-09-11 20:44:17.018][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-11 20:44:17.019][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-11 20:44:17.020][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-11 20:44:17.021][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-11 20:44:17.021][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-11 20:44:17.022][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-11 20:44:17.025][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:17.026][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:17.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:17.031][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:17.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:17.032][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:17.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:17.034][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-09-11 20:44:17.037][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-11 20:44:17.038][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-11 20:44:17.039][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-09-11 20:44:17.426][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-09-11 20:44:17.857][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-11 20:44:17.859][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-09-11 20:44:17.863][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-09-11 20:44:17.865][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-09-11 20:44:17.866][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-11 20:44:17.867][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-11 20:44:17.869][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-11 20:44:17.870][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:17.871][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:17.872][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:17.876][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:17.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:17.878][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:17.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:17.881][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:17.882][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:17.883][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:17.884][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:17.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:17.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:17.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:17.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:17.889][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:17.890][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:17.891][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:17.892][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:17.893][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:17.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:17.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:17.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:17.898][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:17.899][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:17.900][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:17.901][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:17.902][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:17.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:17.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:17.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:17.907][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:17.908][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:17.909][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:17.910][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:17.911][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:17.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:17.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:17.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:17.915][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:17.916][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:17.917][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:17.917][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:17.919][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:17.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:17.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:17.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:17.922][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:17.923][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:17.924][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:17.925][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:17.926][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:17.927][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:17.928][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:17.929][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:17.930][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:17.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:17.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:17.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:17.934][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:17.935][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:17.936][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:17.937][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:17.938][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:17.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:17.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:17.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:17.942][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:17.943][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:17.944][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:17.945][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:17.946][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:17.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:17.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:17.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:17.950][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:17.951][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:17.951][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:17.957][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:17.962][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:17.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:17.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:17.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:17.966][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:17.967][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:17.967][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:17.968][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:17.969][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:17.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:17.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:17.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:17.973][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:17.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:17.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:17.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:17.977][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:17.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:17.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:17.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:17.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:17.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:17.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:17.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:17.985][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:17.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:17.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:17.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:17.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:17.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:17.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:17.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:17.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:17.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:17.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:17.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:17.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:17.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:17.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:17.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:18.011][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-09-11 20:44:18.012][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.016][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.019][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:18.023][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:18.024][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:18.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:18.029][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:18.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:18.030][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:18.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:18.032][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-09-11 20:44:18.033][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-11 20:44:18.035][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-09-11 20:44:18.036][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-11 20:44:18.037][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml".
biodb.DEBUG[2024-09-11 20:44:18.038][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-11 20:44:18.040][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-11 20:44:18.041][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-11 20:44:18.042][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:18.043][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:18.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:18.048][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:18.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:18.050][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:18.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:18.053][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.054][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.055][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.055][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.057][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.060][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:18.061][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:18.062][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.063][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.065][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:18.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:18.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.068][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:18.069][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:18.070][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.071][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.072][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:18.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:18.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.076][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:18.077][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:18.078][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.079][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.080][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:18.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:18.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.084][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:18.085][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:18.085][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.086][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.087][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:18.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:18.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.091][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:18.092][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:18.093][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.094][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.095][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:18.096][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.097][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.098][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.099][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:18.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.103][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:18.104][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:18.105][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.106][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.107][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:18.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:18.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.111][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:18.112][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:18.113][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.114][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.115][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:18.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:18.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.119][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:18.120][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:18.121][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.122][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.127][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:18.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:18.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.131][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:18.132][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:18.133][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.134][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.135][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:18.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:18.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.139][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:18.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:18.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.143][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:18.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:18.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.150][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:18.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:18.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:18.176][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-09-11 20:44:18.177][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.181][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.185][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:18.188][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:18.189][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:18.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:18.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:18.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:18.196][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:18.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:18.198][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-09-11 20:44:18.199][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-11 20:44:18.201][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-09-11 20:44:18.202][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-11 20:44:18.203][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml".
biodb.DEBUG[2024-09-11 20:44:18.205][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-11 20:44:18.206][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-11 20:44:18.207][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-11 20:44:18.209][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:18.210][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:18.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:18.215][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:18.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:18.217][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:18.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:18.220][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.221][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.222][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.223][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.228][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:18.229][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:18.230][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.230][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.232][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:18.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:18.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.235][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:18.236][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:18.237][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.238][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.240][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:18.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:18.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.243][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:18.244][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:18.245][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.246][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.247][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:18.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:18.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.251][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:18.252][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:18.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.254][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.255][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:18.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:18.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.259][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:18.260][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:18.261][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.262][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.263][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:18.264][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.265][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.266][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.267][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:18.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.271][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:18.272][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:18.273][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.274][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.275][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:18.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:18.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.279][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:18.280][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:18.281][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.282][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.283][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:18.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:18.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.287][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:18.288][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:18.289][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.289][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.296][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:18.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:18.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.300][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:18.301][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:18.302][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.303][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.304][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:18.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:18.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.308][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:18.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:18.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.311][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:18.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:18.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.319][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:18.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:18.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.330][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:18.345][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-09-11 20:44:18.346][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.350][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.353][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:18.357][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:18.358][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:18.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:18.363][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:18.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:18.365][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:18.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:18.367][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-09-11 20:44:18.368][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-11 20:44:18.369][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-09-11 20:44:18.370][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-11 20:44:18.372][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml".
biodb.DEBUG[2024-09-11 20:44:18.373][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-11 20:44:18.374][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-11 20:44:18.375][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-11 20:44:18.377][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:18.378][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:18.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:18.383][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:18.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:18.385][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:18.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:18.387][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.388][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.389][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.390][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.395][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:18.396][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:18.397][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.398][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.399][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:18.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:18.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.403][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:18.404][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:18.404][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.405][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.407][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:18.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:18.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.410][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:18.411][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:18.412][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.413][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.414][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:18.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:18.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.418][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:18.419][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:18.420][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.420][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.422][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:18.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:18.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.425][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:18.426][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:18.427][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.428][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.429][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:18.430][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.431][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.432][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.433][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:18.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.437][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:18.438][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:18.439][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.440][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.441][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:18.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:18.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.444][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:18.445][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:18.446][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.447][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.448][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:18.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:18.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.452][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:18.453][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:18.454][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.455][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.461][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:18.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:18.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.465][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:18.466][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:18.467][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.468][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.469][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:18.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:18.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.473][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:18.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:18.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.477][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:18.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:18.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.481][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.484][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:18.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:18.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.492][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:18.510][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-09-11 20:44:18.511][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.515][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.518][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:18.522][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:18.523][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:18.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:18.528][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:18.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:18.530][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:18.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:18.532][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-09-11 20:44:18.533][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-11 20:44:18.534][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-09-11 20:44:18.535][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-11 20:44:18.537][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml".
biodb.DEBUG[2024-09-11 20:44:18.538][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-11 20:44:18.539][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-11 20:44:18.540][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-11 20:44:18.542][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:18.542][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:18.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:18.547][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:18.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:18.549][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:18.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:18.552][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.553][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.554][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.555][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.560][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:18.561][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:18.562][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.562][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.564][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:18.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:18.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.568][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:18.568][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:18.569][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.570][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.571][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:18.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:18.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.575][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:18.576][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:18.577][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.578][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.579][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:18.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:18.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.582][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:18.583][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:18.584][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.585][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.586][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:18.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:18.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.590][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:18.591][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:18.592][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.593][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.594][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:18.595][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.596][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.596][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.598][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:18.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.601][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:18.602][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:18.603][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.604][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.605][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:18.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:18.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.609][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:18.610][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:18.611][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.611][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.613][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:18.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:18.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.616][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:18.617][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:18.618][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.672][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.675][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:18.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:18.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.679][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:18.680][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:18.681][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.682][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.683][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:18.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:18.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.687][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:18.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:18.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.691][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:18.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:18.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.699][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:18.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:18.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.710][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.714][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:18.726][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-09-11 20:44:18.727][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.731][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.734][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:18.738][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:18.739][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:18.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:18.745][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:18.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:18.746][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:18.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:18.748][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-09-11 20:44:18.749][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-11 20:44:18.751][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-09-11 20:44:18.752][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-11 20:44:18.754][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml".
biodb.DEBUG[2024-09-11 20:44:18.755][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-11 20:44:18.756][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-11 20:44:18.757][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-11 20:44:18.759][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:18.759][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:18.760][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:18.765][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:18.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:18.766][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:18.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:18.769][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.770][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.771][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.772][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.777][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:18.778][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:18.779][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.780][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.781][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:18.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:18.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.785][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:18.786][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:18.787][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.788][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.789][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:18.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:18.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.793][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:18.794][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:18.795][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.796][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.797][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:18.798][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:18.799][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.799][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.801][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:18.802][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:18.802][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.803][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.804][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:18.805][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.806][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.807][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.808][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:18.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.812][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:18.813][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:18.814][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.815][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.816][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:18.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:18.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.820][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:18.821][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:18.822][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.822][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.824][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:18.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:18.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.827][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:18.828][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:18.829][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.830][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.831][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:18.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:18.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.835][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:18.836][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:18.837][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.838][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.839][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:18.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:18.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.847][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:18.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:18.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.855][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:18.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:18.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:18.880][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-09-11 20:44:18.881][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.885][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.889][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:18.892][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:18.893][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:18.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:18.898][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:18.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:18.900][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:18.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:18.902][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-09-11 20:44:18.902][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-11 20:44:18.904][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-09-11 20:44:18.905][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-11 20:44:18.906][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml".
biodb.DEBUG[2024-09-11 20:44:18.907][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-11 20:44:18.909][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-11 20:44:18.910][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-11 20:44:18.911][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:18.912][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:18.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:18.917][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:18.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:18.918][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:18.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:18.921][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.922][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.923][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.924][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.929][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:18.930][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:18.931][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.931][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.933][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:18.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:18.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.936][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:18.937][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:18.938][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.939][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.940][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:18.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:18.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.944][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:18.945][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:18.946][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.946][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.948][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:18.949][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:18.949][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.950][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.951][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:18.952][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:18.953][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.954][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.955][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:18.956][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.957][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.958][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.959][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:18.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:18.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.963][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:18.964][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:18.965][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.966][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.967][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:18.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:18.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.970][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:18.971][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:18.972][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.973][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.974][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:18.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:18.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.978][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:18.979][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:18.980][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.981][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.982][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:18.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:18.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.986][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:18.987][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:18.987][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.988][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.990][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:18.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:18.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.993][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:18.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:18.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:18.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:18.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:18.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:18.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.000][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:19.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:19.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:19.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:19.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:19.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:19.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:19.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:19.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:19.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:19.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:19.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:19.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:19.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:19.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:19.031][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-09-11 20:44:19.032][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:19.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:19.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.036][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:19.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:19.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.040][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:19.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:19.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:19.043][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:19.044][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:19.045][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:19.050][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:19.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:19.051][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:19.052][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[2024-09-11 20:44:19.053][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-09-11 20:44:19.054][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-11 20:44:19.056][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-09-11 20:44:19.057][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-11 20:44:19.058][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml".
biodb.DEBUG[2024-09-11 20:44:19.060][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-11 20:44:19.061][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-11 20:44:19.062][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-11 20:44:19.063][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:19.064][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:19.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:19.069][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:19.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:19.071][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:19.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:19.074][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:19.075][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:19.075][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.076][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:19.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:19.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.081][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:19.082][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:19.083][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.084][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.085][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:19.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:19.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.089][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:19.090][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:19.090][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.091][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.092][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:19.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:19.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.096][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:19.097][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:19.098][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.099][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.100][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:19.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:19.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.104][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:19.105][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:19.105][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.106][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.107][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:19.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:19.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.111][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:19.112][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:19.113][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.114][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.115][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:19.116][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:19.117][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.118][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.119][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:19.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:19.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.122][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:19.123][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:19.124][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.125][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.126][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:19.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:19.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.130][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:19.131][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:19.132][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.133][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.134][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:19.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:19.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.138][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:19.139][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:19.140][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.140][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.142][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:19.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:19.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.145][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:19.146][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:19.147][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.148][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.149][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:19.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:19.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.153][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:19.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:19.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.156][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:19.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:19.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:19.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:19.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.163][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:19.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:19.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:19.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:19.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:19.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:19.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:19.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:19.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.183][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:19.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:19.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:19.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:19.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:19.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:19.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:19.194][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-09-11 20:44:19.195][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:19.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:19.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.199][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:19.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:19.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:19.203][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:19.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:19.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:19.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:19.206][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:19.207][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:19.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:19.212][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:19.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:19.214][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:19.215][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[2024-09-11 20:44:19.216][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-09-11 20:44:19.217][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-11 20:44:19.218][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.INFO [2024-09-11 20:44:19.219][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-09-11 20:44:19.220][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-11 20:44:19.221][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-11 20:44:19.222][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-11 20:44:19.223][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-11 20:44:19.224][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-11 20:44:19.225][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-11 20:44:19.228][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:19.228][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:19.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:19.233][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:19.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:19.235][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:19.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:19.237][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2024-09-11 20:44:19.240][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-11 20:44:19.241][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-11 20:44:19.242][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2024-09-11 20:44:19.626][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2024-09-11 20:44:20.010][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-11 20:44:20.014][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2024-09-11 20:44:20.021][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2024-09-11 20:44:20.027][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2024-09-11 20:44:20.030][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-11 20:44:20.033][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-11 20:44:20.035][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-11 20:44:20.039][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:20.040][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:20.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:20.051][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:20.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:20.055][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:20.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:20.060][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:20.062][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:20.063][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:20.065][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:20.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:20.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:20.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:20.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:20.072][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:20.074][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:20.075][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:20.076][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:20.078][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:20.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:20.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:20.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:20.083][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:20.084][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:20.085][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:20.086][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:20.088][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:20.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:20.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:20.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:20.092][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:20.093][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:20.094][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:20.095][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:20.097][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:20.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:20.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:20.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:20.100][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:20.101][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:20.102][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:20.103][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:20.104][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:20.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:20.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:20.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:20.108][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:20.109][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:20.110][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:20.111][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:20.112][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:20.113][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:20.114][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:20.115][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:20.116][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:20.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:20.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:20.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:20.120][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:20.121][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:20.122][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:20.122][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:20.124][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:20.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:20.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:20.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:20.127][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:20.128][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:20.129][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:20.130][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:20.131][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:20.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:20.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:20.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:20.135][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:20.136][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:20.141][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:20.146][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:20.147][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:20.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:20.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:20.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:20.151][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:20.152][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:20.153][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:20.154][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:20.155][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:20.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:20.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:20.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:20.159][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:20.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:20.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:20.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:20.162][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:20.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:20.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:20.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:20.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:20.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:20.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:20.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:20.170][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:20.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:20.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:20.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:20.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:20.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:20.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:20.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:20.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:20.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:20.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:20.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:20.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:20.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:20.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:20.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:20.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:20.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:20.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:20.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:20.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:20.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:20.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:20.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:20.192][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:20.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:20.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:20.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:20.195][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-09-11 20:44:20.196][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:20.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:20.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:20.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:20.200][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:20.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:20.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:20.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:20.204][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:20.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:20.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:20.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:20.207][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:20.208][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:20.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:20.213][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:20.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:20.215][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:20.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:20.217][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-09-11 20:44:20.218][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-11 20:44:20.220][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-09-11 20:44:20.221][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-11 20:44:20.222][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-11 20:44:20.223][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-11 20:44:20.224][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-11 20:44:20.225][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-11 20:44:20.226][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-11 20:44:20.228][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:20.229][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:20.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:20.234][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:20.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:20.236][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:20.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:20.238][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2024-09-11 20:44:20.240][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-11 20:44:20.241][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-11 20:44:20.243][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2024-09-11 20:44:20.634][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2024-09-11 20:44:21.028][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-11 20:44:21.032][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2024-09-11 20:44:21.039][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2024-09-11 20:44:21.045][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2024-09-11 20:44:21.048][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-11 20:44:21.051][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-11 20:44:21.053][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-11 20:44:21.057][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:21.059][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:21.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:21.070][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:21.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:21.073][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:21.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:21.079][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:21.081][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:21.082][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:21.084][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:21.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:21.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:21.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:21.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:21.092][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:21.094][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:21.095][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:21.096][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:21.098][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:21.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:21.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:21.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:21.103][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:21.104][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:21.105][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:21.106][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:21.108][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:21.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:21.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:21.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:21.112][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:21.113][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:21.114][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:21.115][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:21.116][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:21.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:21.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:21.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:21.120][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:21.121][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:21.122][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:21.123][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:21.124][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:21.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:21.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:21.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:21.133][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:21.137][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:21.138][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:21.139][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:21.140][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:21.141][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:21.142][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:21.143][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:21.144][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:21.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:21.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:21.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:21.148][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:21.149][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:21.150][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:21.151][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:21.152][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:21.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:21.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:21.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:21.156][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:21.157][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:21.157][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:21.158][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:21.160][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:21.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:21.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:21.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:21.163][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:21.164][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:21.165][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:21.166][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:21.167][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:21.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:21.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:21.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:21.171][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:21.172][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:21.173][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:21.174][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:21.175][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:21.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:21.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:21.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:21.179][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:21.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:21.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:21.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:21.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:21.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:21.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:21.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:21.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:21.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:21.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:21.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:21.190][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:21.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:21.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:21.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:21.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:21.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:21.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:21.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:21.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:21.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:21.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:21.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:21.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:21.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:21.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:21.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:21.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:21.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:21.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:21.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:21.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:21.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:21.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:21.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:21.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:21.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:21.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:21.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:21.216][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-09-11 20:44:21.217][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:21.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:21.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:21.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:21.220][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:21.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:21.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:21.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:21.224][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:21.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:21.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:21.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:21.228][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:21.229][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:21.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:21.234][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:21.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:21.236][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:21.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:21.238][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-09-11 20:44:21.239][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-11 20:44:21.241][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-09-11 20:44:21.242][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-11 20:44:21.243][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-11 20:44:21.244][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-11 20:44:21.245][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-11 20:44:21.246][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-11 20:44:21.247][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-11 20:44:21.250][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:21.250][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:21.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:21.256][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:21.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:21.257][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:21.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:21.260][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2024-09-11 20:44:21.262][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-11 20:44:21.263][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-11 20:44:21.265][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2024-09-11 20:44:21.651][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2024-09-11 20:44:22.120][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2024-09-11 20:44:22.122][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-09-11 20:44:22.123][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2024-09-11 20:44:22.126][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2024-09-11 20:44:22.131][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2024-09-11 20:44:22.134][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-11 20:44:22.136][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-11 20:44:22.139][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-11 20:44:22.142][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:22.144][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:22.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:22.154][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:22.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:22.158][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:22.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:22.163][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:22.164][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:22.166][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:22.167][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:22.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:22.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:22.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:22.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:22.174][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:22.182][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:22.188][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:22.190][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:22.191][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:22.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:22.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:22.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:22.195][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:22.196][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:22.197][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:22.198][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:22.199][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:22.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:22.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:22.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:22.203][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:22.204][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:22.205][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:22.206][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:22.207][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:22.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:22.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:22.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:22.211][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:22.212][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:22.213][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:22.214][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:22.215][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:22.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:22.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:22.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:22.218][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:22.219][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:22.220][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:22.221][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:22.222][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:22.223][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:22.224][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:22.225][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:22.226][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:22.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:22.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:22.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:22.230][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:22.231][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:22.232][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:22.232][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:22.234][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:22.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:22.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:22.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:22.237][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:22.238][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:22.239][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:22.240][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:22.241][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:22.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:22.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:22.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:22.245][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:22.246][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:22.247][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:22.247][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:22.249][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:22.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:22.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:22.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:22.252][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:22.253][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:22.254][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:22.255][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:22.256][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:22.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:22.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:22.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:22.260][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:22.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:22.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:22.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:22.263][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:22.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:22.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:22.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:22.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:22.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:22.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:22.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:22.271][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:22.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:22.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:22.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:22.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:22.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:22.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:22.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:22.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:22.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:22.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:22.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:22.282][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:22.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:22.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:22.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:22.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:22.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:22.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:22.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:22.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:22.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:22.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:22.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:22.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:22.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:22.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:22.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:22.296][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-09-11 20:44:22.297][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:22.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:22.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:22.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:22.301][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:22.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:22.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:22.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:22.305][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:22.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:22.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:22.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:22.308][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:22.309][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:22.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:22.314][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:22.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:22.316][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:22.317][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[2024-09-11 20:44:22.318][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-09-11 20:44:22.319][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-11 20:44:22.320][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-09-11 20:44:22.321][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-11 20:44:22.322][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-11 20:44:22.323][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-11 20:44:22.324][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-11 20:44:22.325][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-11 20:44:22.326][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-11 20:44:22.329][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:22.329][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:22.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:22.335][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:22.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:22.336][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:22.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:22.338][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2024-09-11 20:44:22.341][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-11 20:44:22.341][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-11 20:44:22.343][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2024-09-11 20:44:22.732][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2024-09-11 20:44:23.122][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-11 20:44:23.140][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2024-09-11 20:44:23.147][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2024-09-11 20:44:23.152][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2024-09-11 20:44:23.155][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-11 20:44:23.158][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-11 20:44:23.160][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-11 20:44:23.164][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:23.165][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:23.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:23.175][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:23.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:23.178][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:23.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:23.182][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:23.184][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:23.185][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:23.187][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:23.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:23.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:23.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:23.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:23.194][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:23.195][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:23.196][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:23.197][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:23.199][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:23.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:23.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:23.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:23.203][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:23.204][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:23.205][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:23.206][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:23.208][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:23.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:23.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:23.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:23.212][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:23.213][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:23.214][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:23.215][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:23.216][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:23.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:23.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:23.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:23.220][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:23.221][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:23.222][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:23.223][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:23.224][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:23.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:23.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:23.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:23.228][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:23.229][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:23.230][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:23.231][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:23.232][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:23.233][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:23.234][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:23.235][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:23.236][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:23.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:23.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:23.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:23.240][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:23.241][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:23.242][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:23.243][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:23.245][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:23.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:23.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:23.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:23.249][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:23.250][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:23.251][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:23.251][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:23.253][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:23.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:23.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:23.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:23.256][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:23.257][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:23.258][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:23.259][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:23.260][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:23.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:23.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:23.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:23.264][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:23.265][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:23.266][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:23.266][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:23.267][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:23.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:23.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:23.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:23.271][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:23.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:23.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:23.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:23.275][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:23.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:23.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:23.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:23.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:23.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:23.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:23.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:23.282][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:23.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:23.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:23.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:23.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:23.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:23.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:23.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:23.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:23.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:23.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:23.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:23.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:23.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:23.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:23.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:23.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:23.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:23.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:23.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:23.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:23.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:23.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:23.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:23.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:23.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:23.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:23.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:23.310][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-09-11 20:44:23.311][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:23.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:23.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:23.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:23.315][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:23.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:23.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:23.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:23.319][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:23.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:23.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:23.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:23.322][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:23.323][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:23.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:23.328][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:23.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:23.330][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:23.335][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[2024-09-11 20:44:23.336][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-09-11 20:44:23.337][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-11 20:44:23.339][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-09-11 20:44:23.340][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-11 20:44:23.341][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-11 20:44:23.342][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-11 20:44:23.343][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-11 20:44:23.344][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-11 20:44:23.344][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-11 20:44:23.347][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:23.348][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:23.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:23.353][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:23.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:23.354][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:23.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:23.356][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2024-09-11 20:44:23.359][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-11 20:44:23.360][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-11 20:44:23.361][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2024-09-11 20:44:23.759][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2024-09-11 20:44:24.168][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-11 20:44:24.172][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2024-09-11 20:44:24.180][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2024-09-11 20:44:24.186][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2024-09-11 20:44:24.189][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-11 20:44:24.192][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-11 20:44:24.194][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-11 20:44:24.198][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:24.200][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:24.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:24.210][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:24.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:24.213][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:24.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:24.218][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:24.219][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:24.221][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:24.222][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:24.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:24.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:24.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:24.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:24.229][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:24.231][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:24.232][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:24.233][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:24.235][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:24.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:24.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:24.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:24.240][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:24.241][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:24.242][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:24.243][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:24.244][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:24.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:24.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:24.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:24.249][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:24.250][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:24.251][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:24.252][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:24.253][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:24.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:24.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:24.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:24.257][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:24.258][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:24.259][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:24.260][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:24.261][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:24.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:24.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:24.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:24.265][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:24.266][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:24.267][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:24.268][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:24.269][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:24.270][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:24.271][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:24.272][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:24.273][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:24.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:24.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:24.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:24.277][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:24.278][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:24.279][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:24.280][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:24.281][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:24.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:24.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:24.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:24.285][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:24.286][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:24.286][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:24.287][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:24.289][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:24.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:24.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:24.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:24.293][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:24.294][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:24.295][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:24.296][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:24.297][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:24.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:24.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:24.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:24.302][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:24.303][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:24.304][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:24.305][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:24.306][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:24.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:24.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:24.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:24.310][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:24.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:24.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:24.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:24.314][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:24.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:24.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:24.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:24.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:24.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:24.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:24.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:24.321][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:24.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:24.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:24.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:24.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:24.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:24.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:24.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:24.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:24.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:24.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:24.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:24.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:24.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:24.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:24.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:24.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:24.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:24.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:24.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:24.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:24.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:24.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:24.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:24.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:24.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:24.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:24.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:24.375][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-09-11 20:44:24.376][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:24.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:24.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:24.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:24.383][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:24.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:24.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:24.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:24.389][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:24.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:24.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:24.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:24.395][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:24.396][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:24.397][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:24.404][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:24.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:24.407][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:24.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:24.410][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-09-11 20:44:24.411][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-11 20:44:24.414][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-09-11 20:44:24.416][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-11 20:44:24.417][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-11 20:44:24.419][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-11 20:44:24.421][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-11 20:44:24.422][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-11 20:44:24.424][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-11 20:44:24.428][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:24.429][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:24.430][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:24.438][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:24.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:24.440][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:24.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:24.444][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2024-09-11 20:44:24.448][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-11 20:44:24.449][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-11 20:44:24.451][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2024-09-11 20:44:24.844][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2024-09-11 20:44:25.269][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-11 20:44:25.273][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2024-09-11 20:44:25.280][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2024-09-11 20:44:25.286][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2024-09-11 20:44:25.289][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-11 20:44:25.292][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-11 20:44:25.294][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-11 20:44:25.298][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:25.300][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:25.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:25.311][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:25.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:25.315][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:25.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:25.320][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:25.322][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:25.323][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:25.325][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:25.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:25.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:25.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:25.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:25.332][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:25.334][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:25.335][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:25.336][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:25.338][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:25.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:25.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:25.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:25.343][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:25.344][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:25.345][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:25.346][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:25.348][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:25.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:25.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:25.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:25.352][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:25.353][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:25.354][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:25.355][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:25.357][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:25.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:25.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:25.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:25.361][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:25.362][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:25.363][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:25.364][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:25.365][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:25.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:25.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:25.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:25.369][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:25.369][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:25.370][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:25.371][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:25.372][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:25.373][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:25.374][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:25.375][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:25.376][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:25.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:25.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:25.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:25.380][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:25.381][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:25.382][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:25.383][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:25.384][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:25.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:25.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:25.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:25.388][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:25.389][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:25.390][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:25.390][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:25.392][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:25.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:25.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:25.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:25.395][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:25.396][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:25.397][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:25.398][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:25.399][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:25.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:25.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:25.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:25.403][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:25.404][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:25.405][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:25.406][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:25.407][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:25.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:25.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:25.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:25.419][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:25.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:25.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:25.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:25.422][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:25.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:25.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:25.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:25.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:25.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:25.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:25.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:25.430][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:25.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:25.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:25.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:25.434][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:25.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:25.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:25.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:25.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:25.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:25.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:25.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:25.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:25.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:25.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:25.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:25.445][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:25.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:25.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:25.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:25.448][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:25.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:25.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:25.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:25.452][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:25.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:25.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:25.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:25.456][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-09-11 20:44:25.457][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:25.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:25.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:25.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:25.460][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:25.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:25.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:25.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:25.464][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:25.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:25.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:25.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:25.483][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[2024-09-11 20:44:25.486][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-11 20:44:25.487][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-11 20:44:25.489][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-09-11 20:44:26.009][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-09-11 20:44:26.554][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-11 20:44:26.558][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-09-11 20:44:26.563][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-09-11 20:44:26.569][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:26.570][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:26.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:26.578][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:26.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:26.581][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:26.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:26.584][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:26.590][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:26.595][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:26.601][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:26.603][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:26.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:26.611][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:26.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:26.613][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:26.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:26.616][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:26.622][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:26.628][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:26.634][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:26.640][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:26.645][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:26.647][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:26.648][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:26.655][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:26.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:26.657][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:26.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:26.660][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:26.666][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:26.672][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:26.676][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:26.679][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:26.692][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:26.693][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:26.694][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:26.698][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:26.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:26.700][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:26.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:26.702][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:26.706][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:26.710][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:26.713][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:26.717][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:26.721][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:26.722][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:26.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:26.727][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:26.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:26.729][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:26.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:26.730][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:26.734][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:26.738][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:26.742][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:26.742][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:26.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:26.748][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:26.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:26.749][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:26.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:26.751][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:26.755][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:26.758][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:26.762][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:26.763][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:26.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:26.768][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:26.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:26.770][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:26.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:26.772][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:26.775][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:26.779][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:26.783][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:26.784][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:26.784][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:26.789][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:26.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:26.790][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:26.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:26.792][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:26.796][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:26.799][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:26.803][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:26.804][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:26.805][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:26.810][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:26.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:26.811][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:26.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:26.813][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:26.817][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:26.821][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:26.825][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:26.825][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:26.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:26.831][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:26.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:26.832][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:26.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:26.834][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:26.838][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:26.842][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:26.845][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:26.846][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:26.847][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:26.851][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:26.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:26.858][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:26.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:26.860][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:26.864][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:26.867][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:26.871][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:26.872][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:26.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:26.877][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:26.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:26.879][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:26.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:26.881][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:26.885][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:26.893][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:26.897][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:26.898][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:26.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:26.905][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:26.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:26.907][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:26.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:26.910][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:26.914][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:26.918][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:26.922][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:26.923][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:26.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:26.928][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:26.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:26.930][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:26.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:26.932][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:26.936][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:26.940][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:26.944][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:26.945][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:26.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:26.951][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:26.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:26.953][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:26.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:26.955][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:26.959][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:26.963][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:26.967][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:26.968][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:26.968][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:26.973][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:26.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:26.975][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:26.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:26.977][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:26.981][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:26.985][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:26.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:26.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:26.989][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:26.990][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:26.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:26.996][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:26.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:26.998][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:26.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:27.000][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:27.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:27.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:27.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:27.004][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:27.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:27.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:27.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:27.008][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:27.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:27.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:27.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:27.012][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:27.013][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:27.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:27.019][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:27.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:27.020][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:27.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:27.022][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:27.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:27.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:27.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:27.026][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:27.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:27.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:27.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:27.030][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:27.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:27.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:27.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:27.034][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:27.049][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:27.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:27.055][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:27.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:27.057][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:27.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:27.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:27.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:27.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:27.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:27.063][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:27.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:27.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:27.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:27.067][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:27.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:27.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:27.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:27.071][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:27.072][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:27.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:27.077][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:27.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:27.079][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:27.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:27.081][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:27.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:27.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:27.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:27.085][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:27.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:27.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:27.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:27.088][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:27.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:27.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:27.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:27.104][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:27.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:27.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:27.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:27.108][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:27.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:27.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:27.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:27.112][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:27.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:27.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:27.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:27.115][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:27.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:27.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:27.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:27.119][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:27.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:27.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:27.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:27.147][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-09-11 20:44:27.150][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-11 20:44:27.151][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-11 20:44:27.153][private$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[2024-09-11 20:44:27.537][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[2024-09-11 20:44:27.922][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-11 20:44:27.926][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2024-09-11 20:44:27.934][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2024-09-11 20:44:27.942][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[2024-09-11 20:44:27.949][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-11 20:44:27.951][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-11 20:44:27.955][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-09-11 20:44:28.374][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-09-11 20:44:28.802][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-11 20:44:28.805][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2024-09-11 20:44:28.810][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2024-09-11 20:44:28.813][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:28.814][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:28.815][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:28.819][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:28.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:28.821][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:28.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:28.822][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-09-11 20:44:28.823][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-11 20:44:28.825][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-09-11 20:44:28.826][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-11 20:44:28.827][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-11 20:44:28.828][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-11 20:44:28.829][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-11 20:44:28.830][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-11 20:44:28.831][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-11 20:44:28.834][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:28.835][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:28.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:28.852][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:28.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:28.854][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:28.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:28.857][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2024-09-11 20:44:28.859][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-11 20:44:28.860][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-11 20:44:28.862][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2024-09-11 20:44:29.255][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2024-09-11 20:44:29.672][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-11 20:44:29.676][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2024-09-11 20:44:29.682][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2024-09-11 20:44:29.686][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2024-09-11 20:44:29.689][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-11 20:44:29.691][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-11 20:44:29.693][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-11 20:44:29.696][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:29.698][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:29.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:29.707][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:29.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:29.710][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:29.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:29.716][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:29.717][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:29.719][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:29.721][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:29.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:29.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:29.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:29.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:29.728][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:29.730][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:29.731][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:29.732][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:29.734][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:29.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:29.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:29.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:29.739][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:29.740][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:29.741][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:29.742][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:29.744][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:29.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:29.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:29.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:29.748][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:29.749][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:29.750][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:29.751][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:29.753][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:29.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:29.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:29.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:29.757][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:29.758][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:29.759][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:29.759][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:29.761][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:29.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:29.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:29.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:29.764][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:29.765][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:29.766][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:29.767][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:29.768][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:29.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:29.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:29.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:29.772][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:29.773][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:29.774][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:29.775][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:29.776][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:29.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:29.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:29.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:29.780][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:29.781][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:29.782][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:29.783][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:29.784][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:29.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:29.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:29.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:29.788][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:29.789][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:29.790][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:29.790][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:29.792][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:29.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:29.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:29.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:29.796][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:29.797][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:29.798][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:29.798][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:29.800][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:29.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:29.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:29.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:29.804][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:29.805][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:29.806][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:29.806][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:29.808][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:29.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:29.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:29.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:29.812][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:29.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:29.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:29.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:29.815][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:29.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:29.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:29.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:29.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:29.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:29.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:29.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:29.823][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:29.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:29.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:29.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:29.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:29.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:29.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:29.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:29.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:29.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:29.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:29.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:29.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:29.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:29.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:29.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:29.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:29.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:29.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:29.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:29.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:29.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:29.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:29.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:29.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:29.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:29.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:29.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:29.850][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-09-11 20:44:29.852][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:29.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:29.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:29.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:29.872][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:29.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:29.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:29.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:29.877][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:29.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:29.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:29.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:29.882][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:29.883][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:29.884][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:29.888][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:29.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:29.890][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:29.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:29.892][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:29.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:29.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:29.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:29.896][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:29.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:29.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:29.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:29.900][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:29.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:29.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:29.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:29.904][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:29.905][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:29.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:29.910][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:29.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:29.912][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:29.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:29.914][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-09-11 20:44:29.915][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-11 20:44:29.917][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-09-11 20:44:29.918][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-11 20:44:29.919][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-11 20:44:29.920][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-11 20:44:29.921][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-11 20:44:29.922][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-11 20:44:29.923][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-11 20:44:29.925][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:29.926][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:29.927][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:29.932][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:29.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:29.933][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:29.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:29.935][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2024-09-11 20:44:29.938][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-11 20:44:29.939][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-11 20:44:29.940][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2024-09-11 20:44:30.334][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2024-09-11 20:44:30.750][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-11 20:44:30.753][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2024-09-11 20:44:30.756][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2024-09-11 20:44:30.758][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2024-09-11 20:44:30.760][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-11 20:44:30.761][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-11 20:44:30.762][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-11 20:44:30.763][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:30.764][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:30.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:30.770][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:30.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:30.772][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:30.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:30.775][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:30.776][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:30.777][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.778][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:30.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:30.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:30.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:30.783][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:30.784][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:30.785][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.786][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:30.788][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:30.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:30.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:30.791][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:30.793][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:30.793][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.794][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:30.796][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:30.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:30.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:30.800][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:30.801][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:30.802][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.803][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:30.804][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:30.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:30.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:30.808][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:30.809][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:30.810][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.810][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:30.812][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:30.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:30.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:30.816][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:30.816][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:30.817][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.818][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:30.819][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:30.820][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:30.821][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.822][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:30.823][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:30.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:30.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:30.827][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:30.828][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:30.829][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.830][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:30.831][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:30.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:30.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:30.835][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:30.836][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:30.837][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.838][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:30.839][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:30.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:30.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:30.843][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:30.844][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:30.845][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.851][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:30.856][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:30.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:30.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:30.860][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:30.861][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:30.861][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.862][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:30.864][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:30.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:30.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:30.867][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:30.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:30.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:30.871][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:30.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:30.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:30.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:30.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:30.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:30.879][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:30.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:30.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:30.882][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:30.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:30.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:30.886][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:30.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:30.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:30.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:30.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:30.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:30.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:30.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:30.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:30.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:30.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:30.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:30.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:30.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:30.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:30.905][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-09-11 20:44:30.906][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:30.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:30.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:30.910][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:30.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:30.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:30.914][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:30.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:30.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:30.934][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-09-11 20:44:30.937][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-11 20:44:30.938][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-09-11 20:44:30.940][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-11 20:44:30.941][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-09-11 20:44:30.945][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:30.946][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:30.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:30.951][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:30.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:30.953][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:30.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:30.955][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:30.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:30.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:30.959][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:30.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:30.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:30.963][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:30.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:30.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:30.966][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:30.967][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:30.968][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:30.973][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:30.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:30.974][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:30.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:30.976][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:30.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:30.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:30.980][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:30.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:30.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:30.984][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:30.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:30.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:30.988][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:30.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:30.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:30.992][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:30.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:30.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:30.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:30.995][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:30.996][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:30.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.001][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.003][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:31.005][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.012][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.016][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.025][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:31.029][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:31.030][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:31.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.035][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.036][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:31.038][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.042][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.046][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.049][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.053][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:31.057][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:31.058][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:31.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.063][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.064][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:31.066][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.070][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.074][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:31.078][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:31.078][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:31.079][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.083][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.085][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:31.087][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.091][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.095][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:31.098][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:31.099][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:31.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.104][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.106][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:31.108][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.112][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.115][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:31.119][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:31.120][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:31.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.125][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.127][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:31.129][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.133][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.137][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:31.141][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:31.142][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:31.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.147][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.149][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:31.151][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.155][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.158][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:31.162][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:31.163][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:31.164][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.168][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.170][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:31.172][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.176][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.180][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:31.183][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:31.184][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:31.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.194][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.196][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:31.198][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.202][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.206][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:31.210][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:31.210][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:31.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.216][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.217][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:31.219][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.223][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.227][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:31.231][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:31.231][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:31.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.236][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.238][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:31.240][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.244][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.247][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:31.251][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:31.252][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:31.253][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.257][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.259][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:31.261][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.265][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.268][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:31.272][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:31.273][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:31.274][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.278][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.280][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:31.282][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.285][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.289][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:31.293][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:31.293][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:31.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.299][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.300][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:31.302][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.306][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.310][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:31.314][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:31.314][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:31.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.320][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.321][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:31.323][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.327][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.331][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:31.334][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:31.335][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:31.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.340][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.342][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:31.344][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.348][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.356][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:31.360][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:31.361][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:31.362][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.366][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.368][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:31.370][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.373][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.377][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:31.381][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:31.382][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:31.383][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.387][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.389][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:31.391][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.395][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.398][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:31.419][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-09-11 20:44:31.422][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-11 20:44:31.424][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-09-11 20:44:31.425][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-11 20:44:31.426][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-09-11 20:44:31.429][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:31.430][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:31.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.435][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.437][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:31.439][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.443][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.446][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:31.450][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:31.451][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:31.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.456][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.458][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:31.460][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.464][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.468][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.471][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.475][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:31.479][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:31.480][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:31.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.485][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.487][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:31.489][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.493][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.496][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.500][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.504][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:31.508][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:31.508][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:31.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.513][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.515][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:31.517][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.527][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.531][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.534][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.538][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:31.542][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:31.543][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:31.544][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.549][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.550][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:31.552][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.556][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.560][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:31.564][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:31.565][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:31.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.570][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.571][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:31.573][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.577][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.581][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:31.585][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:31.585][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:31.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.591][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.592][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:31.594][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.598][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.602][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:31.606][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:31.606][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:31.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.612][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.614][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:31.616][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.619][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.623][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:31.627][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:31.628][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:31.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.633][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.634][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:31.636][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.640][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.644][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:31.648][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:31.648][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:31.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.654][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.655][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:31.657][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.661][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.665][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:31.668][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:31.669][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:31.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.674][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.676][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:31.678][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.681][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.685][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:31.698][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:31.698][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:31.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.704][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.705][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:31.707][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.711][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.715][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:31.719][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:31.719][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:31.720][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.725][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.726][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:31.728][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.736][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:31.740][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:31.740][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:31.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.746][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.747][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:31.749][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.753][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.757][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:31.760][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:31.761][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:31.762][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.766][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.768][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:31.770][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.774][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:31.781][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:31.782][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:31.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.787][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.789][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:31.791][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.794][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.798][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:31.802][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:31.803][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:31.804][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.808][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.810][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:31.812][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.815][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.819][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:31.823][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:31.824][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:31.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.829][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.830][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:31.832][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.836][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.840][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:31.844][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:31.844][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:31.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.849][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.851][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:31.853][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.862][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.866][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:31.870][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:31.871][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:31.872][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.876][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.878][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:31.880][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.884][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.887][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:31.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.903][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-09-11 20:44:31.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-09-11 20:44:31.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-09-11 20:44:31.913][biodb::testThat]
biodb.INFO [2024-09-11 20:44:31.914][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-09-11 20:44:31.915][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-11 20:44:31.916][biodb::testThat]
biodb.TRACE[2024-09-11 20:44:31.919][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-11 20:44:31.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-11 20:44:31.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.922][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:31.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:31.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.926][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:31.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:31.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.930][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:31.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:31.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:31.934][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:31.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:31.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:31.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:31.941][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:31.942][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:31.943][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:31.948][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:31.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:31.949][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:31.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:31.953][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-09-11 20:44:31.956][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-11 20:44:31.957][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-11 20:44:31.959][private$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[2024-09-11 20:44:32.345][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[2024-09-11 20:44:32.752][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-11 20:44:32.755][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-09-11 20:44:32.761][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-09-11 20:44:32.765][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:32.767][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:32.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:32.777][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:32.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:32.780][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:32.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:32.784][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:32.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:32.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:32.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:32.790][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:32.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:32.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:32.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:32.797][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:32.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:32.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:32.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:32.805][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[2024-09-11 20:44:32.809][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-11 20:44:32.811][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-11 20:44:32.813][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-09-11 20:44:33.208][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-09-11 20:44:33.598][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-11 20:44:33.601][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-09-11 20:44:33.604][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-09-11 20:44:33.607][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:33.608][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:33.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:33.613][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:33.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:33.615][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:33.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:33.617][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:33.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:33.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:33.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:33.621][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:33.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:33.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:33.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:33.624][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:33.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:33.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:33.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:33.640][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:33.641][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:33.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:33.646][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:33.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:33.648][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:33.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:33.650][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:33.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:33.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:33.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:33.654][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:33.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:33.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:33.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:33.658][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:33.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:33.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:33.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:33.662][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-09-11 20:44:33.663][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:33.664][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:33.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:33.669][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:33.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:33.671][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:33.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:33.673][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:33.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:33.677][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:33.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:33.681][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:33.682][private$selectFields]
biodb.TRACE[2024-09-11 20:44:33.683][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-11 20:44:33.684][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-11 20:44:33.685][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:33.686][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.687][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.688][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:33.688][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:33.689][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.690][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.691][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:33.692][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:33.693][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:33.694][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:33.695][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.696][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.697][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:33.698][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:33.699][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-11 20:44:33.700][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:33.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:33.704][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:33.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:33.708][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:33.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:33.720][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-09-11 20:44:33.722][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:33.723][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:33.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:33.728][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:33.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:33.730][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:33.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:33.732][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:33.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:33.735][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:33.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:33.739][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:33.740][private$selectFields]
biodb.TRACE[2024-09-11 20:44:33.741][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-11 20:44:33.742][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-11 20:44:33.743][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:33.744][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.745][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.746][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:33.747][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:33.748][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.749][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.750][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:33.751][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:33.752][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:33.753][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:33.755][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.756][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.757][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:33.758][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:33.759][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-11 20:44:33.760][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:33.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:33.764][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:33.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:33.768][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:33.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:33.773][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-09-11 20:44:33.774][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:33.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:33.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:33.780][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:33.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:33.782][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:33.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:33.784][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:33.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:33.788][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:33.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:33.792][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:33.793][private$selectFields]
biodb.TRACE[2024-09-11 20:44:33.794][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-11 20:44:33.795][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-11 20:44:33.796][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:33.797][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.798][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.799][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:33.800][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:33.801][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.802][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.803][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:33.810][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:33.811][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:33.812][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:33.813][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.814][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.815][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:33.816][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:33.817][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-11 20:44:33.818][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:33.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:33.822][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:33.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:33.826][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:33.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:33.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:33.830][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-09-11 20:44:33.831][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-09-11 20:44:33.832][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-09-11 20:44:33.842][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:33.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:33.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:33.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:33.846][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:33.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:33.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:33.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:33.849][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:33.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:33.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:33.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:33.853][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:33.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:33.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:33.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:33.912][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:33.913][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:33.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:33.918][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:33.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:33.920][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:33.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:33.923][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-09-11 20:44:33.927][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-11 20:44:33.928][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-11 20:44:33.929][private$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[2024-09-11 20:44:34.313][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[2024-09-11 20:44:34.703][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-11 20:44:34.708][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2024-09-11 20:44:34.716][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2024-09-11 20:44:34.723][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[2024-09-11 20:44:34.730][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-11 20:44:34.732][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-11 20:44:34.736][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-09-11 20:44:35.160][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-09-11 20:44:35.542][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-11 20:44:35.545][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2024-09-11 20:44:35.549][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2024-09-11 20:44:35.553][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:35.554][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:35.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:35.615][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:35.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:35.640][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:35.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:35.644][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:35.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:35.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:35.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:35.649][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:35.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:35.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:35.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:35.655][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:35.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:35.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:35.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:35.660][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:35.662][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:35.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:35.673][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:35.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:35.675][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:35.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:35.678][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:35.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:35.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:35.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:35.682][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:35.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:35.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:35.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:35.703][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:35.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:35.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:35.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:35.708][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:35.709][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:35.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:35.731][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:35.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:35.734][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:35.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:35.736][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:35.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:35.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:35.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:35.757][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:35.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:35.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:35.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:35.761][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:35.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:35.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:35.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:35.850][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-09-11 20:44:35.879][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:35.880][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:35.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:35.887][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:35.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:35.889][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:35.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:35.891][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:35.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:35.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:35.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:35.896][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:35.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:35.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:35.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:35.900][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:35.902][private$selectFields]
biodb.TRACE[2024-09-11 20:44:35.903][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-11 20:44:35.904][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-11 20:44:35.905][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:35.906][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:35.907][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:35.908][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:35.909][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:35.910][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:35.912][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:35.913][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:35.914][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:35.915][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:35.916][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:35.917][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:35.918][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:35.919][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:35.920][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:35.921][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-11 20:44:35.922][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:35.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:35.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:35.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:35.927][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:35.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:35.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:35.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:35.939][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:35.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:35.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:35.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:35.945][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-09-11 20:44:35.946][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:35.947][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:35.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:35.953][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:35.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:35.955][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:35.956][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.TRACE[2024-09-11 20:44:35.972][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:35.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:35.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:35.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:35.976][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:35.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:35.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:35.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.006][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.007][private$selectFields]
biodb.TRACE[2024-09-11 20:44:36.009][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-11 20:44:36.010][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-11 20:44:36.011][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.012][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.013][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.014][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.016][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.017][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.018][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.019][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.020][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.021][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.034][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.035][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.037][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.038][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.039][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.040][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-11 20:44:36.041][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.046][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.050][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.055][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-09-11 20:44:36.056][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:36.057][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:36.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:36.064][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:36.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:36.066][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:36.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:36.068][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.073][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.077][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.078][private$selectFields]
biodb.TRACE[2024-09-11 20:44:36.079][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-11 20:44:36.080][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-11 20:44:36.081][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.083][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.084][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.085][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.086][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.087][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.088][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.089][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.090][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.092][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.093][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.094][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.095][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.096][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.097][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.098][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-11 20:44:36.099][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.104][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.108][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.113][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-09-11 20:44:36.114][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-09-11 20:44:36.115][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-09-11 20:44:36.133][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-09-11 20:44:36.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-09-11 20:44:36.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-09-11 20:44:36.141][biodb::testThat]
biodb.INFO [2024-09-11 20:44:36.142][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-09-11 20:44:36.144][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-11 20:44:36.145][biodb::testThat]
biodb.TRACE[2024-09-11 20:44:36.148][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-11 20:44:36.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-11 20:44:36.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.153][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.158][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.163][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.168][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:36.176][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:36.177][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:36.178][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:36.183][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:36.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:36.185][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:36.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:36.188][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-09-11 20:44:36.191][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-11 20:44:36.193][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-09-11 20:44:36.194][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-11 20:44:36.195][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-09-11 20:44:36.197][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:36.198][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:36.199][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:36.204][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:36.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:36.205][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:36.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:36.207][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.211][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.215][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:36.220][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-09-11 20:44:36.223][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-11 20:44:36.224][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-09-11 20:44:36.225][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-11 20:44:36.226][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-09-11 20:44:36.229][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:36.229][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:36.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:36.235][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:36.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:36.236][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:36.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:36.238][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.242][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.246][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:36.250][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:36.251][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:36.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:36.256][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:36.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:36.258][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:36.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:36.260][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.264][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.268][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:36.272][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-09-11 20:44:36.273][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:36.274][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:36.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:36.280][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:36.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:36.282][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:36.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:36.284][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.288][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.292][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.292][private$selectFields]
biodb.TRACE[2024-09-11 20:44:36.293][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-11 20:44:36.294][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-11 20:44:36.295][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.296][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.297][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.298][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.299][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.300][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.301][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.302][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.303][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.304][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.305][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.313][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.314][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.316][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.317][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.318][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-11 20:44:36.319][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.323][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.327][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.331][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-09-11 20:44:36.332][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:36.333][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:36.334][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:36.339][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:36.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:36.340][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:36.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:36.343][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.346][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.350][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.351][private$selectFields]
biodb.TRACE[2024-09-11 20:44:36.352][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-11 20:44:36.353][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-11 20:44:36.354][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.355][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.356][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.357][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.357][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.358][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.359][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.360][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.361][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.362][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.363][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.364][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.365][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.366][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.367][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.368][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-11 20:44:36.369][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.372][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.376][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.380][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-09-11 20:44:36.381][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:36.382][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:36.383][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:36.387][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:36.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:36.389][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:36.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:36.391][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.394][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.398][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.399][private$selectFields]
biodb.TRACE[2024-09-11 20:44:36.400][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-11 20:44:36.401][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-11 20:44:36.402][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.403][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.404][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.405][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.405][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.406][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.407][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.408][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.409][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.410][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.411][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.412][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.413][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.414][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.414][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.415][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-11 20:44:36.416][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.420][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.424][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.428][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-09-11 20:44:36.429][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-09-11 20:44:36.430][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-09-11 20:44:36.437][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:36.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:36.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.442][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:36.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:36.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.445][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:36.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:36.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.449][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:36.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:36.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:36.455][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:36.456][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:36.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:36.461][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:36.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:36.463][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:36.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:36.466][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-09-11 20:44:36.469][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-11 20:44:36.471][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-09-11 20:44:36.472][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-11 20:44:36.474][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-09-11 20:44:36.483][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-09-11 20:44:36.487][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-11 20:44:36.488][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-09-11 20:44:36.489][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-11 20:44:36.491][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-09-11 20:44:36.493][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:36.494][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:36.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:36.499][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:36.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:36.501][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:36.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:36.503][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:36.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:36.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.507][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:36.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:36.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.510][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:36.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:36.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:36.514][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:36.515][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:36.516][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:36.520][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:36.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:36.522][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:36.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:36.524][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:36.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:36.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.528][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:36.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:36.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.532][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:36.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:36.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:36.536][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:36.537][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:36.538][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:36.542][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:36.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:36.544][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:36.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:36.545][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:36.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:36.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.549][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:36.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:36.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.553][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:36.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:36.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:36.557][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-09-11 20:44:36.558][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:36.559][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:36.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:36.564][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:36.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:36.566][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:36.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:36.568][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.571][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.575][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.576][private$selectFields]
biodb.TRACE[2024-09-11 20:44:36.577][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-11 20:44:36.578][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-11 20:44:36.579][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.580][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.581][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.581][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.582][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.583][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.584][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.585][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.586][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.587][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.588][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.589][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.590][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.591][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.591][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.592][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-11 20:44:36.593][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.597][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.601][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.605][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-09-11 20:44:36.606][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:36.607][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:36.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:36.612][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:36.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:36.614][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:36.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:36.616][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.619][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.623][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.624][private$selectFields]
biodb.TRACE[2024-09-11 20:44:36.625][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-11 20:44:36.626][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-11 20:44:36.627][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.628][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.629][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.629][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.630][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.631][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.632][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.633][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.634][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.635][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.636][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.637][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.638][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.639][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.639][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.640][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-11 20:44:36.641][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.654][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.661][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.667][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-09-11 20:44:36.668][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:36.669][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:36.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:36.677][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:36.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:36.679][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:36.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:36.682][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.686][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.690][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.691][private$selectFields]
biodb.TRACE[2024-09-11 20:44:36.692][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-11 20:44:36.693][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-11 20:44:36.694][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.695][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.696][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.697][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.698][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.700][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.701][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.702][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.703][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.704][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.705][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.706][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.707][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.708][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.709][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.710][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-11 20:44:36.711][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.715][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.719][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.723][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-09-11 20:44:36.724][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-09-11 20:44:36.725][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-09-11 20:44:36.734][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-09-11 20:44:36.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-09-11 20:44:36.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-09-11 20:44:36.742][biodb::testThat]
biodb.INFO [2024-09-11 20:44:36.743][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-09-11 20:44:36.744][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-11 20:44:36.745][biodb::testThat]
biodb.TRACE[2024-09-11 20:44:36.748][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-11 20:44:36.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-11 20:44:36.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.752][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.756][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.760][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.764][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:36.773][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:36.774][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:36.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:36.779][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:36.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:36.781][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:36.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:36.785][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-09-11 20:44:36.789][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-11 20:44:36.790][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-09-11 20:44:36.792][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-11 20:44:36.793][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-09-11 20:44:36.796][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:36.797][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:36.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:36.803][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:36.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:36.805][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:36.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:36.807][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.811][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.815][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:36.820][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-09-11 20:44:36.823][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-11 20:44:36.824][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-09-11 20:44:36.825][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-11 20:44:36.827][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-09-11 20:44:36.829][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:36.830][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:36.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:36.836][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:36.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:36.838][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:36.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:36.854][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.858][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.862][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:36.866][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:36.867][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:36.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:36.873][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:36.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:36.874][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:36.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:36.876][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.880][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.884][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:36.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:36.888][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-09-11 20:44:36.890][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:36.890][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:36.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:36.896][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:36.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:36.898][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:36.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:36.900][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.904][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.908][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.909][private$selectFields]
biodb.TRACE[2024-09-11 20:44:36.909][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-11 20:44:36.910][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-11 20:44:36.911][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.912][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.913][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.914][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.915][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.916][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.917][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.918][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.919][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.920][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.921][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.922][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.923][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.924][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.925][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.926][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-11 20:44:36.927][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.930][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.935][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.939][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-09-11 20:44:36.940][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:36.941][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:36.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:36.946][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:36.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:36.948][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:36.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:36.950][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.954][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.958][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.959][private$selectFields]
biodb.TRACE[2024-09-11 20:44:36.960][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-11 20:44:36.961][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-11 20:44:36.962][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.963][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.964][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.964][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.965][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.966][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.967][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.968][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.969][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.970][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.971][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:36.972][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.973][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.974][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.975][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.976][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-11 20:44:36.977][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.981][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.984][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:36.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:36.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:36.988][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-09-11 20:44:36.990][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:36.990][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:36.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:36.996][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:36.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:36.998][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:36.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:37.000][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.004][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.007][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:37.008][private$selectFields]
biodb.TRACE[2024-09-11 20:44:37.009][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-11 20:44:37.010][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-11 20:44:37.011][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:37.012][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.013][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.014][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.015][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.016][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.022][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.023][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.024][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.025][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:37.026][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:37.027][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.028][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.029][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.029][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.030][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-11 20:44:37.031][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.035][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.039][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.043][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-09-11 20:44:37.044][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-09-11 20:44:37.045][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-09-11 20:44:37.061][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:37.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:37.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.065][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:37.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:37.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.069][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:37.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:37.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.073][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:37.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:37.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:37.080][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:37.081][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:37.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:37.086][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:37.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:37.087][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:37.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:37.091][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-09-11 20:44:37.094][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-11 20:44:37.095][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-09-11 20:44:37.096][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-11 20:44:37.097][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-09-11 20:44:37.100][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-09-11 20:44:37.103][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-11 20:44:37.104][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-09-11 20:44:37.105][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-11 20:44:37.107][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-09-11 20:44:37.109][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:37.110][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:37.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:37.115][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:37.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:37.116][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:37.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:37.118][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:37.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:37.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.122][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:37.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:37.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.126][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:37.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:37.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:37.130][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:37.130][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:37.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:37.135][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:37.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:37.137][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:37.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:37.139][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:37.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:37.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.143][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:37.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:37.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.147][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:37.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:37.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:37.150][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:37.151][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:37.152][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:37.156][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:37.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:37.158][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:37.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:37.160][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:37.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:37.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.164][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:37.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:37.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.167][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:37.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:37.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:37.171][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-09-11 20:44:37.173][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:37.173][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:37.174][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:37.178][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:37.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:37.185][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:37.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:37.188][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.192][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.195][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:37.196][private$selectFields]
biodb.TRACE[2024-09-11 20:44:37.197][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-11 20:44:37.198][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-11 20:44:37.199][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:37.200][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.201][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.202][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.203][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.204][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.205][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.205][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.206][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.207][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:37.208][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:37.209][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.210][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.211][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.212][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.213][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-11 20:44:37.214][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.217][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.221][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.225][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-09-11 20:44:37.226][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:37.227][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:37.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:37.232][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:37.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:37.233][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:37.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:37.235][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.239][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.243][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:37.244][private$selectFields]
biodb.TRACE[2024-09-11 20:44:37.244][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-11 20:44:37.245][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-11 20:44:37.246][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:37.247][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.248][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.249][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.250][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.251][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.252][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.252][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.253][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.254][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:37.255][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:37.256][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.257][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.258][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.259][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.260][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-11 20:44:37.261][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.264][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.268][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.272][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-09-11 20:44:37.273][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:37.274][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:37.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:37.279][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:37.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:37.280][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:37.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:37.282][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.286][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.290][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:37.291][private$selectFields]
biodb.TRACE[2024-09-11 20:44:37.291][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-11 20:44:37.292][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-11 20:44:37.293][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:37.294][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.295][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.296][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.297][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.298][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.299][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.300][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.301][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.301][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:37.302][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-11 20:44:37.303][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.304][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.305][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.306][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.307][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-11 20:44:37.308][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.312][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.315][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:37.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:37.319][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-09-11 20:44:37.320][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-09-11 20:44:37.321][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-09-11 20:44:37.338][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-09-11 20:44:37.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-09-11 20:44:37.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:37.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-09-11 20:44:37.351][biodb::testThat]
biodb.INFO [2024-09-11 20:44:37.352][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-09-11 20:44:37.352][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-11 20:44:37.353][biodb::testThat]
biodb.DEBUG[2024-09-11 20:44:37.355][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-09-11 20:44:37.356][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-11 20:44:37.357][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-09-11 20:44:37.359][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-11 20:44:37.360][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-11 20:44:37.361][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-11 20:44:37.362][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-11 20:44:37.363][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-11 20:44:37.364][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-11 20:44:37.366][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:37.367][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:37.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:37.372][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:37.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:37.374][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:37.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:37.376][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2024-09-11 20:44:37.378][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-11 20:44:37.379][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-11 20:44:37.380][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2024-09-11 20:44:37.764][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2024-09-11 20:44:38.156][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-11 20:44:38.159][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2024-09-11 20:44:38.162][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2024-09-11 20:44:38.164][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2024-09-11 20:44:38.166][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-11 20:44:38.167][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-11 20:44:38.168][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-11 20:44:38.169][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:38.170][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:38.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:38.175][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:38.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:38.177][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:38.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:38.180][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:38.181][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:38.182][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:38.183][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:38.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:38.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:38.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:38.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:38.187][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:38.188][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:38.189][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:38.190][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:38.191][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:38.192][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:38.193][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:38.194][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:38.195][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:38.196][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:38.197][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:38.198][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:38.199][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:38.200][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:38.201][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:38.202][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:38.203][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:38.204][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:38.205][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:38.206][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:38.207][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:38.208][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:38.209][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:38.210][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:38.211][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:38.212][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:38.213][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:38.214][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:38.215][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:38.216][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:38.217][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:38.218][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:38.219][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:38.220][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:38.221][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:38.222][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:38.223][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:38.224][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:38.225][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:38.226][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:38.227][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:38.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:38.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:38.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:38.230][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:38.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:38.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:38.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:38.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:38.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:38.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:38.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:38.238][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:38.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:38.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:38.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:38.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:38.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:38.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:38.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:38.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:38.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:38.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:38.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:38.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:38.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:38.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:38.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:38.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:38.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:38.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:38.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:38.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:38.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:38.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:38.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:38.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:38.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:38.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:38.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:38.268][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-09-11 20:44:38.269][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-09-11 20:44:38.276][biodb::testThat]
biodb.INFO [2024-09-11 20:44:38.277][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-09-11 20:44:38.278][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-11 20:44:38.279][biodb::testThat]
biodb.DEBUG[2024-09-11 20:44:38.297][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-09-11 20:44:38.298][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-09-11 20:44:38.299][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-09-11 20:44:38.301][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-09-11 20:44:38.302][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2024-09-11 20:44:38.303][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-11 20:44:38.304][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-11 20:44:38.305][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-11 20:44:38.306][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-11 20:44:38.307][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-11 20:44:38.311][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:38.311][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:38.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:38.317][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:38.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:38.318][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:38.319][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[2024-09-11 20:44:38.320][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2024-09-11 20:44:38.323][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-11 20:44:38.324][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-11 20:44:38.325][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2024-09-11 20:44:38.712][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2024-09-11 20:44:39.135][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-11 20:44:39.139][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2024-09-11 20:44:39.146][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2024-09-11 20:44:39.148][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:39.150][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:39.152][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:39.160][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:39.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:39.163][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:39.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:39.167][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2024-09-11 20:44:39.172][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-11 20:44:39.174][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-11 20:44:39.177][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2024-09-11 20:44:40.717][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2024-09-11 20:44:41.117][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-11 20:44:41.121][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2024-09-11 20:44:41.129][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2024-09-11 20:44:41.131][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:41.133][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:41.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:41.145][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:41.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:41.149][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:41.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:41.154][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2024-09-11 20:44:41.159][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-11 20:44:41.161][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-11 20:44:41.164][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2024-09-11 20:44:41.578][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2024-09-11 20:44:42.007][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-11 20:44:42.011][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2024-09-11 20:44:42.018][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2024-09-11 20:44:42.024][private$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[2024-09-11 20:44:42.027][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-11 20:44:42.030][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-09-11 20:44:42.032][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-09-11 20:44:42.036][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:42.038][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:42.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:42.049][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:42.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:42.052][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:42.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:42.058][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:42.060][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:42.061][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.063][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:42.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:42.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.071][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:42.072][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:42.073][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.075][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.076][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:42.077][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:42.079][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.080][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.081][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:42.083][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:42.084][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.085][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.086][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:42.087][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:42.088][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.089][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.091][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:42.092][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:42.093][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.094][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.095][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:42.096][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:42.097][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.098][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.099][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:42.100][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:42.101][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.102][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.103][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:42.104][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:42.105][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.106][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.107][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:42.108][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:42.109][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.110][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.111][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:42.112][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:42.113][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.114][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.115][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:42.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:42.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.118][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:42.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:42.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:42.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:42.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.140][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:42.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:42.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:42.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:42.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:42.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:42.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:42.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:42.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:42.155][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:42.156][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:42.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:42.161][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:42.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:42.162][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:42.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:42.165][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:42.166][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:42.167][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.168][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:42.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:42.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.173][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:42.174][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:42.175][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.175][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.177][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:42.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:42.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.180][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:42.181][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:42.182][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.183][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.184][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:42.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:42.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.188][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:42.189][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:42.190][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.191][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.192][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:42.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:42.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.195][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:42.196][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:42.197][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.198][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.199][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:42.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:42.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.203][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:42.204][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:42.205][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.206][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.207][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:42.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:42.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.211][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:42.212][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:42.212][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.213][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.214][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:42.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:42.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.218][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:42.219][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:42.220][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.221][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.222][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:42.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:42.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.226][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:42.226][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:42.227][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.228][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.229][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:42.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:42.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.233][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:42.234][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:42.235][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.236][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.237][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:42.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:42.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.241][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:42.241][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:42.242][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.243][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.244][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:42.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:42.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.248][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:42.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:42.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.252][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:42.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:42.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:42.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:42.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.259][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:42.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:42.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:42.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:42.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:42.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:42.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:42.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:42.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:42.274][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:42.275][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:42.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:42.280][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:42.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:42.282][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:42.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:42.284][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:42.285][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:42.291][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.292][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:42.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:42.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.298][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:42.299][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:42.300][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.300][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.302][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:42.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:42.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.305][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:42.306][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:42.307][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.308][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.309][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:42.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:42.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.313][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:42.314][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:42.315][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.316][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.317][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:42.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:42.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.320][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:42.321][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:42.322][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.323][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.324][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:42.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:42.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.328][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:42.329][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:42.330][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.331][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.332][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:42.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:42.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.336][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:42.336][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:42.337][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.338][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.339][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:42.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:42.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.343][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:42.344][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:42.345][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.346][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.347][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:42.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:42.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.350][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:42.351][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:42.352][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.353][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.354][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:42.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:42.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.358][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:42.359][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:42.360][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.361][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.362][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:42.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:42.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.366][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:42.367][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:42.367][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.368][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.369][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:42.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:42.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.373][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:42.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:42.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.377][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:42.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:42.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:42.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:42.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.384][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:42.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:42.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:42.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:42.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:42.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:42.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.395][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:42.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:42.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:42.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:42.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:42.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:42.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.407][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:42.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:42.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:42.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:42.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:42.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:42.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.418][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:42.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:42.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:42.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:42.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:42.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:42.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:42.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:42.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:42.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:42.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:42.432][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-09-11 20:44:42.433][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-09-11 20:44:42.434][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-09-11 20:44:42.451][biodb::testThat]
biodb.INFO [2024-09-11 20:44:42.452][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-09-11 20:44:42.453][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-11 20:44:42.454][biodb::testThat]
biodb.INFO [2024-09-11 20:44:42.476][biodb::testThat]
biodb.INFO [2024-09-11 20:44:42.477][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-09-11 20:44:42.478][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-11 20:44:42.479][biodb::testThat]
biodb.INFO [2024-09-11 20:44:42.487][biodb::testThat]
biodb.INFO [2024-09-11 20:44:42.488][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-09-11 20:44:42.489][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-11 20:44:42.490][biodb::testThat]
biodb.DEBUG[2024-09-11 20:44:42.492][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2024-09-11 20:44:42.495][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-11 20:44:42.496][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-11 20:44:42.498][private$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[2024-09-11 20:44:42.953][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[2024-09-11 20:44:43.492][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-11 20:44:43.497][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2024-09-11 20:44:43.505][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2024-09-11 20:44:43.527][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:43.530][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:43.532][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:43.534][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:43.536][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:43.538][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:43.540][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:43.541][ef$get] fields variable is a list.
biodb.INFO [2024-09-11 20:44:43.544][biodb::testThat]
biodb.INFO [2024-09-11 20:44:43.545][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-09-11 20:44:43.547][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-11 20:44:43.548][biodb::testThat]
biodb.ERROR[2024-09-11 20:44:43.566][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-09-11 20:44:43.584][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-09-11 20:44:43.596][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-09-11 20:44:43.597][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-09-11 20:44:43.598][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-09-11 20:44:43.599][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-09-11 20:44:43.600][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:43.601][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:43.602][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:43.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:43.603][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:43.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-09-11 20:44:43.613][biodb::testContext]
biodb.INFO [2024-09-11 20:44:43.614][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-11 20:44:43.615][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-09-11 20:44:43.616][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-11 20:44:43.617][biodb::testContext]
biodb.INFO [2024-09-11 20:44:43.619][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-09-11 20:44:43.620][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-09-11 20:44:43.624][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-11 20:44:43.625][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-09-11 20:44:43.626][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-09-11 20:44:43.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:43.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:43.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:43.629][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-09-11 20:44:43.630][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-09-11 20:44:43.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:43.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:43.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:43.642][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-09-11 20:44:43.644][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-09-11 20:44:43.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:43.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:43.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:43.648][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-09-11 20:44:43.649][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-09-11 20:44:43.650][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-09-11 20:44:43.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:43.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:43.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:43.653][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-09-11 20:44:43.654][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-09-11 20:44:43.655][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-09-11 20:44:43.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:43.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:43.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:43.658][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-09-11 20:44:43.659][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-09-11 20:44:43.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:43.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:43.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:43.663][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-09-11 20:44:43.664][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-09-11 20:44:43.665][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-09-11 20:44:43.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:43.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:43.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:43.668][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-09-11 20:44:43.669][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-09-11 20:44:43.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:43.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:43.672][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[2024-09-11 20:44:43.673][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-09-11 20:44:43.674][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-09-11 20:44:43.675][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-09-11 20:44:43.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:43.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:43.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:43.678][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-09-11 20:44:43.679][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-09-11 20:44:43.680][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-09-11 20:44:43.681][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-09-11 20:44:43.682][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-09-11 20:44:43.683][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-09-11 20:44:43.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:43.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:43.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:43.686][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-09-11 20:44:43.687][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-09-11 20:44:43.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:43.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:43.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:43.690][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-09-11 20:44:43.691][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-09-11 20:44:43.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:43.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:43.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:43.695][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-09-11 20:44:43.696][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-09-11 20:44:43.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:43.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:43.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:43.699][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-09-11 20:44:43.700][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-09-11 20:44:43.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:43.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:43.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:43.703][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-09-11 20:44:43.704][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-09-11 20:44:43.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:43.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:43.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:43.707][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-09-11 20:44:43.708][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-09-11 20:44:43.711][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-09-11 20:44:43.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:43.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:43.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:43.715][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-09-11 20:44:43.715][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-09-11 20:44:43.716][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-09-11 20:44:43.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:43.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:43.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:43.720][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-09-11 20:44:43.722][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:43.723][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-09-11 20:44:43.723][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:43.724][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-11 20:44:43.725][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:43.726][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-11 20:44:43.727][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:43.728][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-11 20:44:43.729][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-09-11 20:44:43.730][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-11 20:44:43.731][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:43.732][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-09-11 20:44:43.733][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-11 20:44:43.734][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:43.734][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:43.735][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-11 20:44:43.735][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-11 20:44:43.735][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-11 20:44:43.735][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-09-11 20:44:43.735][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-09-11 20:44:43.736][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-11 20:44:43.737][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:43.738][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:43.739][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-11 20:44:43.740][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:43.741][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:43.741][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-11 20:44:43.742][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:43.743][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-11 20:44:43.744][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-11 20:44:43.745][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:43.746][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:43.747][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-09-11 20:44:43.748][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:43.749][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-09-11 20:44:43.750][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:43.751][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-11 20:44:43.752][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:43.753][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-11 20:44:43.754][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:43.755][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-11 20:44:43.756][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-09-11 20:44:43.757][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-11 20:44:43.758][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:43.759][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-09-11 20:44:43.760][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-11 20:44:43.761][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:43.761][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:43.762][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-11 20:44:43.762][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-11 20:44:43.762][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-11 20:44:43.762][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-09-11 20:44:43.762][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-09-11 20:44:43.763][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-11 20:44:43.764][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:43.765][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:43.766][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-11 20:44:43.767][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:43.768][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:43.769][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-11 20:44:43.769][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:43.770][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-11 20:44:43.771][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-11 20:44:43.772][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:43.773][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:43.774][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-09-11 20:44:43.776][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:43.777][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-09-11 20:44:43.778][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:43.778][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-11 20:44:43.779][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:43.780][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-11 20:44:43.781][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:43.782][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-11 20:44:43.783][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-09-11 20:44:43.784][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-11 20:44:43.785][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:43.786][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-09-11 20:44:43.787][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-11 20:44:43.788][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:43.789][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:43.789][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:43.790][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-11 20:44:43.791][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:43.792][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:43.798][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-11 20:44:43.800][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:43.801][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:43.802][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-11 20:44:43.803][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:43.804][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-11 20:44:43.804][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-11 20:44:43.805][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:43.806][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:43.807][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-09-11 20:44:43.809][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:43.810][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-09-11 20:44:43.811][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:43.812][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-11 20:44:43.813][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:43.814][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-11 20:44:43.814][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:43.815][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-11 20:44:43.816][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-09-11 20:44:43.817][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-11 20:44:43.818][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:43.819][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-09-11 20:44:43.820][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-11 20:44:43.821][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:43.822][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:43.823][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:43.824][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-11 20:44:43.825][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:43.826][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:43.827][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-11 20:44:43.828][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:43.828][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:43.829][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-11 20:44:43.830][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:43.831][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-11 20:44:43.832][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-11 20:44:43.833][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:43.834][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:43.835][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-11 20:44:43.836][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:43.836][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[2024-09-11 20:44:43.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:43.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:43.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:43.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:43.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:43.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:43.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:43.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:43.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:43.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:43.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:43.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:43.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:43.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:43.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:43.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:43.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:43.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:43.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:43.853][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[2024-09-11 20:44:43.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:43.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:43.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:43.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:43.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:43.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:43.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:43.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:43.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:43.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:43.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:43.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:43.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:43.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:43.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:43.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:43.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:43.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:43.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:43.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:43.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:43.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:43.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:43.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:43.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:43.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:43.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:43.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:43.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:43.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:43.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:43.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:43.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:43.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:43.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:43.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:43.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:43.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:43.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:43.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:43.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:43.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:43.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:43.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:43.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:43.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:43.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:43.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:43.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:43.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:43.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:43.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:43.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:43.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:43.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:43.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:43.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:43.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:43.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:43.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:43.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:43.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:43.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:43.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:43.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:43.907][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-09-11 20:44:43.908][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-09-11 20:44:43.909][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-09-11 20:44:43.911][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-09-11 20:44:43.912][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-09-11 20:44:43.913][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-09-11 20:44:43.914][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-09-11 20:44:43.916][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-09-11 20:44:43.917][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-09-11 20:44:43.918][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-09-11 20:44:43.920][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-09-11 20:44:43.921][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-09-11 20:44:43.922][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-09-11 20:44:43.923][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-09-11 20:44:43.925][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-09-11 20:44:43.926][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-09-11 20:44:43.927][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-09-11 20:44:43.929][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-09-11 20:44:43.930][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-09-11 20:44:43.931][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-09-11 20:44:43.932][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-09-11 20:44:43.934][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-09-11 20:44:43.935][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-09-11 20:44:43.936][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-09-11 20:44:43.937][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-09-11 20:44:43.939][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-09-11 20:44:43.940][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-09-11 20:44:43.941][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-09-11 20:44:43.943][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-09-11 20:44:43.944][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-09-11 20:44:43.951][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-09-11 20:44:43.953][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-09-11 20:44:43.954][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-09-11 20:44:43.956][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-09-11 20:44:43.957][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-09-11 20:44:43.958][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-09-11 20:44:43.959][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-09-11 20:44:43.961][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-09-11 20:44:43.962][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-09-11 20:44:43.963][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-09-11 20:44:43.965][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-09-11 20:44:43.966][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-09-11 20:44:43.967][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-09-11 20:44:43.969][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-09-11 20:44:43.970][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-09-11 20:44:43.971][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-09-11 20:44:43.972][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-09-11 20:44:43.974][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-09-11 20:44:43.975][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-09-11 20:44:43.976][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-09-11 20:44:43.978][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-09-11 20:44:43.979][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-09-11 20:44:43.980][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-09-11 20:44:43.981][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-09-11 20:44:43.983][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-09-11 20:44:43.984][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-09-11 20:44:43.985][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-09-11 20:44:43.987][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-09-11 20:44:43.988][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-09-11 20:44:43.989][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-09-11 20:44:43.990][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-09-11 20:44:43.992][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-09-11 20:44:43.993][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-09-11 20:44:43.994][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-09-11 20:44:43.996][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-09-11 20:44:43.997][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-09-11 20:44:43.998][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-09-11 20:44:43.999][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-09-11 20:44:44.001][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-09-11 20:44:44.002][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-09-11 20:44:44.003][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-09-11 20:44:44.005][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-09-11 20:44:44.006][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-09-11 20:44:44.007][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-09-11 20:44:44.008][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-09-11 20:44:44.010][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-09-11 20:44:44.011][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-09-11 20:44:44.012][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-09-11 20:44:44.014][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-09-11 20:44:44.015][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-09-11 20:44:44.016][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-09-11 20:44:44.017][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-09-11 20:44:44.019][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-09-11 20:44:44.020][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-09-11 20:44:44.022][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-09-11 20:44:44.023][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-11 20:44:44.023][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:44.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:44.025][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:44.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:44.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:44.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:44.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:44.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:44.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:44.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:44.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:44.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:44.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:44.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:44.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:44.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:44.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:44.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:44.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:44.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:44.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:44.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:44.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:44.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:44.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:44.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:44.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:44.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:44.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:44.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:44.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:44.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:44.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:44.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:44.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:44.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:44.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:44.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:44.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:44.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:44.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:44.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:44.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:44.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:44.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:44.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:44.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:44.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:44.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:44.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:44.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:44.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:44.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:44.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:44.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:44.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:44.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:44.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:44.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:44.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:44.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:44.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:44.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:44.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:44.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:44.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:44.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:44.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:44.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:44.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:44.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:44.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:44.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:44.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:44.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:44.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:44.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:44.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:44.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:44.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:44.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:44.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:44.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:44.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:44.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:44.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:44.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:44.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:44.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:44.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:44.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:44.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:44.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:44.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:44.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:44.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:44.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:44.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:44.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:44.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:44.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:44.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:44.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:44.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:44.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:44.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:44.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:44.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:44.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:44.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:44.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:44.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:44.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:44.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:44.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:44.305][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[2024-09-11 20:44:44.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:44.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:44.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:44.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:44.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:44.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:44.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:44.312][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-09-11 20:44:44.313][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-09-11 20:44:44.315][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:44.316][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-09-11 20:44:44.317][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:44.318][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-11 20:44:44.319][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:44.319][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-11 20:44:44.320][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:44.321][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-09-11 20:44:44.322][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-09-11 20:44:44.323][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-11 20:44:44.324][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:44.325][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-09-11 20:44:44.326][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-11 20:44:44.327][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-09-11 20:44:44.327][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-09-11 20:44:44.327][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-09-11 20:44:44.327][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-09-11 20:44:44.327][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-09-11 20:44:44.327][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-09-11 20:44:44.327][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-09-11 20:44:44.327][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-09-11 20:44:44.327][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-09-11 20:44:44.327][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-09-11 20:44:44.327][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-09-11 20:44:44.328][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:44.329][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-11 20:44:44.329][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-11 20:44:44.329][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-11 20:44:44.329][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-09-11 20:44:44.330][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:44.331][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:44.332][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-11 20:44:44.333][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:44.334][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:44.334][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-11 20:44:44.335][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-11 20:44:44.335][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-09-11 20:44:44.336][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-11 20:44:44.337][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-11 20:44:44.338][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:44.339][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-09-11 20:44:44.339][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-09-11 20:44:44.340][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-09-11 20:44:44.341][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-09-11 20:44:44.343][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-09-11 20:44:44.344][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-09-11 20:44:44.346][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-09-11 20:44:44.347][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-09-11 20:44:44.350][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-09-11 20:44:44.351][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-09-11 20:44:44.352][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-09-11 20:44:44.353][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-09-11 20:44:44.354][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-11 20:44:44.355][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-11 20:44:44.356][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-09-11 20:44:44.357][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-09-11 20:44:44.359][biodb::testThat]
biodb.INFO [2024-09-11 20:44:44.360][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2024-09-11 20:44:44.360][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-11 20:44:44.361][biodb::testThat]
biodb.DEBUG[2024-09-11 20:44:44.365][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-09-11 20:44:44.368][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-11 20:44:44.369][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-11 20:44:44.370][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2024-09-11 20:44:44.747][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2024-09-11 20:44:45.306][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-11 20:44:45.310][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2024-09-11 20:44:45.318][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2024-09-11 20:44:45.326][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-09-11 20:44:45.333][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-11 20:44:45.335][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-11 20:44:45.339][private$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[2024-09-11 20:44:45.758][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[2024-09-11 20:44:46.187][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-11 20:44:46.191][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2024-09-11 20:44:46.199][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2024-09-11 20:44:46.204][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:46.206][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:46.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:46.217][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:46.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:46.221][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:46.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:46.226][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[2024-09-11 20:44:46.233][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-11 20:44:46.234][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-11 20:44:46.237][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-09-11 20:44:46.648][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-09-11 20:44:47.079][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-11 20:44:47.083][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2024-09-11 20:44:47.089][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2024-09-11 20:44:47.093][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:47.094][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:47.096][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:47.103][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:47.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:47.106][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:47.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:47.136][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:47.137][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:47.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:47.144][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:47.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:47.146][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:47.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:47.153][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-09-11 20:44:47.156][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-11 20:44:47.158][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-09-11 20:44:47.159][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-11 20:44:47.160][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-09-11 20:44:47.162][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:47.163][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:47.164][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:47.168][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:47.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:47.170][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:47.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:47.173][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-09-11 20:44:47.176][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-11 20:44:47.178][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-09-11 20:44:47.179][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-11 20:44:47.180][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-09-11 20:44:47.182][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:47.183][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:47.184][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:47.188][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:47.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:47.190][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:47.191][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[2024-09-11 20:44:47.192][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:47.193][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:47.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:47.198][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:47.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:47.200][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:47.201][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[2024-09-11 20:44:47.205][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-09-11 20:44:47.208][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-11 20:44:47.209][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-09-11 20:44:47.211][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-11 20:44:47.212][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-09-11 20:44:47.214][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:47.215][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:47.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:47.220][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:47.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:47.222][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:47.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:47.225][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-09-11 20:44:47.228][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-11 20:44:47.229][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-09-11 20:44:47.230][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-11 20:44:47.232][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-09-11 20:44:47.234][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:47.234][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:47.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:47.240][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:47.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:47.242][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:47.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:47.244][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-09-11 20:44:47.248][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-11 20:44:47.249][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-11 20:44:47.250][private$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[2024-09-11 20:44:47.636][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[2024-09-11 20:44:48.028][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-11 20:44:48.030][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2024-09-11 20:44:48.035][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2024-09-11 20:44:48.037][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:48.038][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:48.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:48.044][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:48.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:48.046][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:48.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-09-11 20:44:48.054][biodb::testThat]
biodb.INFO [2024-09-11 20:44:48.055][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2024-09-11 20:44:48.056][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-11 20:44:48.073][biodb::testThat]
biodb.DEBUG[2024-09-11 20:44:48.077][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[2024-09-11 20:44:48.080][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-11 20:44:48.081][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-11 20:44:48.083][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-09-11 20:44:48.468][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-09-11 20:44:48.851][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-11 20:44:48.853][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2024-09-11 20:44:48.857][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2024-09-11 20:44:48.859][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:48.860][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:48.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:48.865][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:48.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:48.866][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:48.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:48.871][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-09-11 20:44:48.874][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-11 20:44:48.875][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-11 20:44:48.877][private$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[2024-09-11 20:44:49.259][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[2024-09-11 20:44:49.679][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-11 20:44:49.684][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2024-09-11 20:44:49.692][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2024-09-11 20:44:49.696][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:49.698][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:49.700][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:49.709][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:49.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:49.713][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:49.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-09-11 20:44:49.724][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-09-11 20:44:49.726][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-09-11 20:44:49.728][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-09-11 20:44:49.730][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-09-11 20:44:49.731][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:49.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:49.734][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:49.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:49.737][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:49.738][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.INFO [2024-09-11 20:44:49.743][biodb::testContext]
biodb.INFO [2024-09-11 20:44:49.744][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-11 20:44:49.745][biodb::testContext] Test context - Test web services
biodb.INFO [2024-09-11 20:44:49.746][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-11 20:44:49.748][biodb::testContext]
biodb.INFO [2024-09-11 20:44:49.750][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-09-11 20:44:49.752][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-09-11 20:44:49.757][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-11 20:44:49.758][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-09-11 20:44:49.759][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-09-11 20:44:49.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:49.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:49.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:49.763][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-09-11 20:44:49.764][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-09-11 20:44:49.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:49.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:49.766][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[2024-09-11 20:44:49.767][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-09-11 20:44:49.768][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-09-11 20:44:49.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:49.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:49.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:49.772][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-09-11 20:44:49.773][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-09-11 20:44:49.774][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-09-11 20:44:49.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:49.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:49.776][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[2024-09-11 20:44:49.777][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-09-11 20:44:49.778][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-09-11 20:44:49.779][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-09-11 20:44:49.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:49.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:49.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:49.782][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-09-11 20:44:49.783][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-09-11 20:44:49.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:49.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:49.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:49.786][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-09-11 20:44:49.787][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-09-11 20:44:49.788][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-09-11 20:44:49.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:49.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:49.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:49.791][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-09-11 20:44:49.792][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-09-11 20:44:49.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:49.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:49.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:49.795][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-09-11 20:44:49.796][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-09-11 20:44:49.797][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-09-11 20:44:49.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:49.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:49.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:49.800][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-09-11 20:44:49.801][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-09-11 20:44:49.802][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-09-11 20:44:49.803][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-09-11 20:44:49.804][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-09-11 20:44:49.805][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-09-11 20:44:49.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:49.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:49.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:49.808][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-09-11 20:44:49.809][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-09-11 20:44:49.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:49.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:49.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:49.812][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-09-11 20:44:49.813][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-09-11 20:44:49.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:49.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:49.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:49.816][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-09-11 20:44:49.817][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-09-11 20:44:49.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:49.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:49.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:49.821][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-09-11 20:44:49.822][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-09-11 20:44:49.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:49.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:49.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:49.825][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-09-11 20:44:49.826][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-09-11 20:44:49.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:49.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:49.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:49.829][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-09-11 20:44:49.830][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-09-11 20:44:49.834][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-09-11 20:44:49.835][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:49.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:49.836][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[2024-09-11 20:44:49.837][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-09-11 20:44:49.838][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-09-11 20:44:49.839][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-09-11 20:44:49.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:49.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:49.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:49.843][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-09-11 20:44:49.844][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:49.845][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-09-11 20:44:49.846][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:49.847][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-11 20:44:49.848][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:49.849][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-11 20:44:49.850][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:49.851][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-11 20:44:49.851][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-09-11 20:44:49.852][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-11 20:44:49.853][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:49.854][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-09-11 20:44:49.855][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-11 20:44:49.856][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:49.857][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:49.858][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-11 20:44:49.858][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-11 20:44:49.858][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-11 20:44:49.858][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-09-11 20:44:49.858][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-09-11 20:44:49.859][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-11 20:44:49.859][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:49.860][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:49.861][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-11 20:44:49.862][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:49.863][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:49.864][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-11 20:44:49.865][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:49.865][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-11 20:44:49.866][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-11 20:44:49.867][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:49.868][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:49.869][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-09-11 20:44:49.871][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:49.872][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-09-11 20:44:49.872][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:49.873][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-11 20:44:49.874][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:49.875][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-11 20:44:49.876][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:49.877][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-11 20:44:49.878][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-09-11 20:44:49.879][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-11 20:44:49.880][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:49.881][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-09-11 20:44:49.882][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-11 20:44:49.882][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:49.883][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:49.884][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-11 20:44:49.884][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-11 20:44:49.884][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-11 20:44:49.884][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-09-11 20:44:49.884][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-09-11 20:44:49.885][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-11 20:44:49.886][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:49.887][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:49.888][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-11 20:44:49.889][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:49.889][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:49.890][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-11 20:44:49.891][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:49.892][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-11 20:44:49.893][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-11 20:44:49.894][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:49.895][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:49.896][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-09-11 20:44:49.898][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:49.898][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-09-11 20:44:49.899][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:49.900][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-11 20:44:49.901][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:49.902][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-11 20:44:49.903][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:49.904][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-11 20:44:49.905][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-09-11 20:44:49.906][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-11 20:44:49.907][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:49.908][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-09-11 20:44:49.908][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-11 20:44:49.909][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:49.910][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:49.911][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:49.912][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-11 20:44:49.913][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:49.914][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:49.915][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-11 20:44:49.916][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:49.916][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:49.917][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-11 20:44:49.918][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:49.919][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-11 20:44:49.920][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-11 20:44:49.921][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:49.922][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:49.923][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-09-11 20:44:49.924][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:49.925][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-09-11 20:44:49.926][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:49.927][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-11 20:44:49.928][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:49.929][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-11 20:44:49.930][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:49.931][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-11 20:44:49.931][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-09-11 20:44:49.932][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-11 20:44:49.933][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:49.934][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-09-11 20:44:49.935][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-11 20:44:49.936][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:49.937][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:49.938][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:49.939][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-11 20:44:49.939][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:49.940][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:49.941][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-11 20:44:49.942][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:49.943][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:49.944][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-11 20:44:49.945][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:49.945][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-11 20:44:49.946][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-11 20:44:49.947][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:49.948][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:49.949][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-11 20:44:49.950][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:49.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:49.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:49.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:49.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:49.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:49.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:49.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:49.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:49.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:49.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:49.959][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[2024-09-11 20:44:49.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:49.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:49.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:49.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:49.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:49.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:49.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:49.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:49.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:49.977][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[2024-09-11 20:44:49.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:49.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:49.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:49.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:49.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:49.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:49.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:49.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:49.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:49.985][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[2024-09-11 20:44:49.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:49.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:49.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:49.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:49.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:49.990][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:49.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:49.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:49.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:49.993][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[2024-09-11 20:44:49.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:49.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:49.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:49.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:49.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:49.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:49.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:49.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:50.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:50.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:50.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:50.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:50.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:50.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:50.005][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[2024-09-11 20:44:50.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:50.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:50.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:50.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:50.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:50.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:50.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:50.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:50.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:50.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:50.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:50.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:50.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:50.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:50.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:50.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:50.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:50.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:50.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:50.022][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.DEBUG[2024-09-11 20:44:50.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:50.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:50.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:50.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:50.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:50.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:50.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:50.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:50.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:50.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:50.031][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-09-11 20:44:50.032][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-09-11 20:44:50.034][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-09-11 20:44:50.035][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-09-11 20:44:50.036][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-09-11 20:44:50.037][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-09-11 20:44:50.039][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-09-11 20:44:50.040][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-09-11 20:44:50.041][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-09-11 20:44:50.042][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-09-11 20:44:50.043][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-09-11 20:44:50.045][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-09-11 20:44:50.046][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-09-11 20:44:50.047][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-09-11 20:44:50.048][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-09-11 20:44:50.050][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-09-11 20:44:50.051][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-09-11 20:44:50.052][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-09-11 20:44:50.053][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-09-11 20:44:50.055][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-09-11 20:44:50.056][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-09-11 20:44:50.057][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-09-11 20:44:50.058][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-09-11 20:44:50.060][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-09-11 20:44:50.061][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-09-11 20:44:50.062][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-09-11 20:44:50.063][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-09-11 20:44:50.064][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-09-11 20:44:50.066][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-09-11 20:44:50.067][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-09-11 20:44:50.068][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-09-11 20:44:50.069][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-09-11 20:44:50.071][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-09-11 20:44:50.072][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-09-11 20:44:50.073][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-09-11 20:44:50.074][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-09-11 20:44:50.075][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-09-11 20:44:50.077][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-09-11 20:44:50.078][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-09-11 20:44:50.079][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-09-11 20:44:50.080][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-09-11 20:44:50.082][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-09-11 20:44:50.083][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-09-11 20:44:50.084][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-09-11 20:44:50.085][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-09-11 20:44:50.087][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-09-11 20:44:50.088][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-09-11 20:44:50.089][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-09-11 20:44:50.090][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-09-11 20:44:50.092][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-09-11 20:44:50.093][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-09-11 20:44:50.094][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-09-11 20:44:50.096][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-09-11 20:44:50.097][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-09-11 20:44:50.098][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-09-11 20:44:50.099][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-09-11 20:44:50.101][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-09-11 20:44:50.102][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-09-11 20:44:50.103][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-09-11 20:44:50.104][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-09-11 20:44:50.106][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-09-11 20:44:50.107][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-09-11 20:44:50.108][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-09-11 20:44:50.109][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-09-11 20:44:50.111][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-09-11 20:44:50.112][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-09-11 20:44:50.113][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-09-11 20:44:50.114][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-09-11 20:44:50.116][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-09-11 20:44:50.117][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-09-11 20:44:50.118][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-09-11 20:44:50.119][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-09-11 20:44:50.121][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-09-11 20:44:50.122][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-09-11 20:44:50.123][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-09-11 20:44:50.125][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-09-11 20:44:50.126][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-09-11 20:44:50.127][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-09-11 20:44:50.128][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-09-11 20:44:50.130][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-09-11 20:44:50.131][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-09-11 20:44:50.132][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-09-11 20:44:50.133][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-09-11 20:44:50.135][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-09-11 20:44:50.136][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-09-11 20:44:50.137][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-11 20:44:50.138][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:50.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:50.139][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:50.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:50.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:50.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:50.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:50.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:50.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:50.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:50.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:50.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:50.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:50.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:50.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:50.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:50.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:50.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:50.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:50.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:50.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:50.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:50.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:50.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:50.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:50.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:50.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:50.159][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:50.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:50.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:50.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:50.163][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.DEBUG[2024-09-11 20:44:50.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:50.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:50.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:50.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:50.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:50.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:50.168][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[2024-09-11 20:44:50.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:50.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:50.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:50.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:50.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:50.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:50.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:50.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:50.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:50.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:50.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:50.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:50.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:50.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:50.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:50.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:50.182][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:50.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:50.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:50.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:50.185][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[2024-09-11 20:44:50.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:50.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:50.187][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:50.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:50.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:50.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:50.191][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[2024-09-11 20:44:50.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:50.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:50.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:50.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:50.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:50.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:50.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:50.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:50.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:50.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:50.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:50.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:50.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:50.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:50.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:50.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:50.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:50.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:50.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:50.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:50.214][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[2024-09-11 20:44:50.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:50.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:50.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:50.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:50.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:50.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:50.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:50.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:50.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:50.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:50.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:50.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:50.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:50.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:50.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:50.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:50.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:50.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:50.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:50.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:50.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:50.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:50.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:50.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:50.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:50.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:50.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:50.247][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[2024-09-11 20:44:50.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:50.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:50.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:50.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:50.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:50.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:50.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:50.258][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-09-11 20:44:50.260][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-09-11 20:44:50.263][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:50.265][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-09-11 20:44:50.266][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:50.276][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-11 20:44:50.277][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:50.279][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-11 20:44:50.280][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:50.281][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-09-11 20:44:50.283][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-09-11 20:44:50.284][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-11 20:44:50.286][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:50.287][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-09-11 20:44:50.288][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-11 20:44:50.290][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-09-11 20:44:50.290][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-09-11 20:44:50.290][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-09-11 20:44:50.290][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-09-11 20:44:50.290][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-09-11 20:44:50.290][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-09-11 20:44:50.290][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-09-11 20:44:50.290][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-09-11 20:44:50.290][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-09-11 20:44:50.290][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-09-11 20:44:50.290][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-09-11 20:44:50.292][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:50.293][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-11 20:44:50.293][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-11 20:44:50.293][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-11 20:44:50.294][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-09-11 20:44:50.296][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:50.297][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:50.298][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-11 20:44:50.300][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:50.301][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:50.302][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-11 20:44:50.304][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-11 20:44:50.304][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-09-11 20:44:50.305][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-11 20:44:50.306][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-11 20:44:50.308][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:50.309][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-09-11 20:44:50.309][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-09-11 20:44:50.311][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-09-11 20:44:50.313][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-09-11 20:44:50.316][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-09-11 20:44:50.318][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-09-11 20:44:50.320][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-09-11 20:44:50.322][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-09-11 20:44:50.327][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-09-11 20:44:50.328][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-09-11 20:44:50.329][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-09-11 20:44:50.330][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-09-11 20:44:50.331][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-11 20:44:50.332][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-11 20:44:50.333][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-09-11 20:44:50.334][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-09-11 20:44:50.335][biodb::testThat]
biodb.INFO [2024-09-11 20:44:50.336][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-09-11 20:44:50.337][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-11 20:44:50.338][biodb::testThat]
biodb.DEBUG[2024-09-11 20:44:50.341][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-09-11 20:44:50.344][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-11 20:44:50.345][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-09-11 20:44:50.346][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-11 20:44:50.347][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-09-11 20:44:50.350][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[2024-09-11 20:44:50.353][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-11 20:44:50.354][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-11 20:44:50.356][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-09-11 20:44:50.740][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-09-11 20:44:51.148][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-11 20:44:51.153][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2024-09-11 20:44:51.161][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2024-09-11 20:44:51.177][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-09-11 20:44:51.180][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-09-11 20:44:51.182][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-09-11 20:44:51.184][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-09-11 20:44:51.186][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:51.188][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:51.190][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:51.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:51.193][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-09-11 20:44:51.200][biodb::testContext]
biodb.INFO [2024-09-11 20:44:51.202][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-11 20:44:51.204][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-09-11 20:44:51.205][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-11 20:44:51.206][biodb::testContext]
biodb.INFO [2024-09-11 20:44:51.209][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-09-11 20:44:51.212][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-09-11 20:44:51.217][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-11 20:44:51.218][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-09-11 20:44:51.220][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-09-11 20:44:51.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.224][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-09-11 20:44:51.225][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-09-11 20:44:51.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.229][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-09-11 20:44:51.230][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-09-11 20:44:51.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.234][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-09-11 20:44:51.235][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-09-11 20:44:51.236][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-09-11 20:44:51.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.239][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-09-11 20:44:51.240][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-09-11 20:44:51.241][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-09-11 20:44:51.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.244][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-09-11 20:44:51.245][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-09-11 20:44:51.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.249][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-09-11 20:44:51.249][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-09-11 20:44:51.250][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-09-11 20:44:51.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.253][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[2024-09-11 20:44:51.254][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-09-11 20:44:51.255][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-09-11 20:44:51.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.258][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-09-11 20:44:51.259][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-09-11 20:44:51.260][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-09-11 20:44:51.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.263][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-09-11 20:44:51.264][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-09-11 20:44:51.265][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-09-11 20:44:51.266][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-09-11 20:44:51.267][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-09-11 20:44:51.268][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-09-11 20:44:51.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.271][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-09-11 20:44:51.272][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-09-11 20:44:51.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.276][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-09-11 20:44:51.277][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-09-11 20:44:51.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.280][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-09-11 20:44:51.281][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-09-11 20:44:51.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.284][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-09-11 20:44:51.285][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-09-11 20:44:51.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.288][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-09-11 20:44:51.289][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-09-11 20:44:51.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.293][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-09-11 20:44:51.294][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-09-11 20:44:51.297][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-09-11 20:44:51.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.301][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-09-11 20:44:51.302][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-09-11 20:44:51.303][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-09-11 20:44:51.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.305][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[2024-09-11 20:44:51.306][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-09-11 20:44:51.308][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:51.309][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-09-11 20:44:51.309][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:51.310][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-11 20:44:51.311][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:51.312][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-11 20:44:51.313][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:51.314][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-11 20:44:51.315][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-09-11 20:44:51.316][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-11 20:44:51.317][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:51.317][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-09-11 20:44:51.318][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-11 20:44:51.319][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:51.320][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:51.321][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-11 20:44:51.321][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-11 20:44:51.321][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-11 20:44:51.321][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-09-11 20:44:51.321][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-09-11 20:44:51.322][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-11 20:44:51.323][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:51.324][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:51.324][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-11 20:44:51.325][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:51.326][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:51.327][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-11 20:44:51.328][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:51.329][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-11 20:44:51.330][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-11 20:44:51.330][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:51.331][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:51.332][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-09-11 20:44:51.334][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:51.335][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-09-11 20:44:51.336][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:51.337][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-11 20:44:51.338][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:51.339][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-11 20:44:51.340][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:51.340][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-11 20:44:51.341][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-09-11 20:44:51.342][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-11 20:44:51.343][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:51.344][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-09-11 20:44:51.345][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-11 20:44:51.346][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:51.347][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:51.348][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-11 20:44:51.348][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-11 20:44:51.348][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-11 20:44:51.348][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-09-11 20:44:51.348][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-09-11 20:44:51.349][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-11 20:44:51.350][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:51.350][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:51.351][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-11 20:44:51.352][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:51.353][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:51.354][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-11 20:44:51.355][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:51.356][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-11 20:44:51.356][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-11 20:44:51.357][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:51.358][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:51.359][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-09-11 20:44:51.361][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:51.362][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-09-11 20:44:51.363][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:51.364][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-11 20:44:51.365][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:51.365][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-11 20:44:51.366][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:51.367][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-11 20:44:51.368][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-09-11 20:44:51.369][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-11 20:44:51.370][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:51.371][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-09-11 20:44:51.372][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-11 20:44:51.373][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:51.374][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:51.375][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:51.375][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-11 20:44:51.376][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:51.377][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:51.378][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-11 20:44:51.379][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:51.380][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:51.381][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-11 20:44:51.381][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:51.382][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-11 20:44:51.383][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-11 20:44:51.384][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:51.385][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:51.386][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-09-11 20:44:51.388][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:51.389][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-09-11 20:44:51.389][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:51.390][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-11 20:44:51.391][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:51.392][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-11 20:44:51.393][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:51.394][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-11 20:44:51.395][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-09-11 20:44:51.396][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-11 20:44:51.397][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:51.398][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-09-11 20:44:51.398][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-11 20:44:51.399][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:51.400][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:51.401][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:51.402][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-11 20:44:51.403][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:51.404][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:51.405][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-11 20:44:51.406][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:51.415][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:51.416][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-11 20:44:51.417][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:51.418][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-11 20:44:51.419][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-11 20:44:51.420][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:51.421][self$setPropertyValue]
biodb.DEBUG[2024-09-11 20:44:51.422][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-11 20:44:51.423][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.423][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[2024-09-11 20:44:51.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:51.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:51.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.427][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.DEBUG[2024-09-11 20:44:51.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:51.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:51.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:51.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:51.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.435][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[2024-09-11 20:44:51.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:51.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:51.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:51.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:51.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.443][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[2024-09-11 20:44:51.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:51.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:51.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.447][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[2024-09-11 20:44:51.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:51.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:51.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.451][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[2024-09-11 20:44:51.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:51.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:51.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.455][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[2024-09-11 20:44:51.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:51.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:51.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:51.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:51.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:51.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:51.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:51.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:51.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:51.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:51.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:51.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:51.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:51.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:51.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.484][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[2024-09-11 20:44:51.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:51.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:51.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:51.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:51.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.492][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-09-11 20:44:51.494][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-09-11 20:44:51.495][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-09-11 20:44:51.496][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-09-11 20:44:51.497][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-09-11 20:44:51.499][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-09-11 20:44:51.500][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-09-11 20:44:51.501][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-09-11 20:44:51.502][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-09-11 20:44:51.504][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-09-11 20:44:51.505][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-09-11 20:44:51.506][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-09-11 20:44:51.507][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-09-11 20:44:51.509][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-09-11 20:44:51.510][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-09-11 20:44:51.511][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-09-11 20:44:51.512][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-09-11 20:44:51.514][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-09-11 20:44:51.515][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-09-11 20:44:51.516][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-09-11 20:44:51.517][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-09-11 20:44:51.519][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-09-11 20:44:51.520][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-09-11 20:44:51.521][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-09-11 20:44:51.522][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-09-11 20:44:51.524][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-09-11 20:44:51.525][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-09-11 20:44:51.526][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-09-11 20:44:51.528][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-09-11 20:44:51.529][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-09-11 20:44:51.530][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-09-11 20:44:51.531][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-09-11 20:44:51.533][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-09-11 20:44:51.534][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-09-11 20:44:51.535][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-09-11 20:44:51.536][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-09-11 20:44:51.538][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-09-11 20:44:51.539][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-09-11 20:44:51.540][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-09-11 20:44:51.541][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-09-11 20:44:51.543][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-09-11 20:44:51.544][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-09-11 20:44:51.545][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-09-11 20:44:51.547][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-09-11 20:44:51.548][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-09-11 20:44:51.549][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-09-11 20:44:51.550][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-09-11 20:44:51.552][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-09-11 20:44:51.553][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-09-11 20:44:51.554][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-09-11 20:44:51.556][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-09-11 20:44:51.557][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-09-11 20:44:51.558][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-09-11 20:44:51.559][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-09-11 20:44:51.561][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-09-11 20:44:51.562][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-09-11 20:44:51.563][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-09-11 20:44:51.564][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-09-11 20:44:51.566][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-09-11 20:44:51.567][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-09-11 20:44:51.568][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-09-11 20:44:51.570][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-09-11 20:44:51.571][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-09-11 20:44:51.572][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-09-11 20:44:51.573][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-09-11 20:44:51.575][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-09-11 20:44:51.576][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-09-11 20:44:51.577][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-09-11 20:44:51.578][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-09-11 20:44:51.580][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-09-11 20:44:51.581][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-09-11 20:44:51.582][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-09-11 20:44:51.584][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-09-11 20:44:51.585][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-09-11 20:44:51.586][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-09-11 20:44:51.587][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-09-11 20:44:51.589][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-09-11 20:44:51.590][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-09-11 20:44:51.591][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-09-11 20:44:51.593][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-09-11 20:44:51.594][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-09-11 20:44:51.595][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-09-11 20:44:51.596][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-09-11 20:44:51.598][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-09-11 20:44:51.599][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-09-11 20:44:51.600][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-11 20:44:51.601][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:51.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:51.603][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:51.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:51.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:51.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:51.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:51.612][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:51.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:51.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:51.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:51.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:51.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:51.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:51.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:51.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:51.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:51.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:51.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:51.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:51.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:51.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:51.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:51.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:51.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:51.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:51.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:51.646][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:51.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:51.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:51.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:51.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:51.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:51.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:51.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:51.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:51.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:51.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:51.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.663][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[2024-09-11 20:44:51.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:51.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:51.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:51.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:51.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:51.672][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:51.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:51.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:51.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:51.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:51.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:51.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:51.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:51.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:51.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:51.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:51.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:51.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:51.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:51.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:51.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:51.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:51.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:51.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:51.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:51.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:51.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:51.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:51.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-11 20:44:51.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:51.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:51.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:51.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:51.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.734][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-09-11 20:44:51.736][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-09-11 20:44:51.738][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:51.739][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-09-11 20:44:51.740][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:51.741][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-11 20:44:51.742][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:51.743][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-11 20:44:51.744][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:51.745][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-09-11 20:44:51.746][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-09-11 20:44:51.747][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-11 20:44:51.748][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:51.749][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-09-11 20:44:51.750][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-11 20:44:51.751][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-09-11 20:44:51.751][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-09-11 20:44:51.751][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-09-11 20:44:51.751][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-09-11 20:44:51.751][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-09-11 20:44:51.751][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-09-11 20:44:51.751][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-09-11 20:44:51.751][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-09-11 20:44:51.751][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-09-11 20:44:51.751][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-09-11 20:44:51.751][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-09-11 20:44:51.752][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-09-11 20:44:51.753][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-11 20:44:51.753][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-11 20:44:51.753][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-11 20:44:51.754][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-09-11 20:44:51.755][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:51.755][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:51.756][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-11 20:44:51.757][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-11 20:44:51.758][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-11 20:44:51.759][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-11 20:44:51.760][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-11 20:44:51.760][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-09-11 20:44:51.761][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-11 20:44:51.762][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-11 20:44:51.763][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-09-11 20:44:51.764][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-09-11 20:44:51.764][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-09-11 20:44:51.765][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-09-11 20:44:51.767][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-09-11 20:44:51.768][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-09-11 20:44:51.770][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-09-11 20:44:51.771][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-09-11 20:44:51.773][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-09-11 20:44:51.776][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-09-11 20:44:51.777][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-09-11 20:44:51.778][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-09-11 20:44:51.780][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-09-11 20:44:51.781][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-11 20:44:51.782][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-11 20:44:51.783][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-09-11 20:44:51.784][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-09-11 20:44:51.786][biodb::testThat]
biodb.INFO [2024-09-11 20:44:51.787][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-09-11 20:44:51.788][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-11 20:44:51.788][biodb::testThat]
biodb.DEBUG[2024-09-11 20:44:51.792][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-09-11 20:44:51.795][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-11 20:44:51.797][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-09-11 20:44:51.798][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-11 20:44:51.799][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-09-11 20:44:51.803][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-09-11 20:44:51.806][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-11 20:44:51.807][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-09-11 20:44:51.808][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-11 20:44:51.810][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-09-11 20:44:51.814][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-09-11 20:44:51.815][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-11 20:44:51.816][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-09-11 20:44:51.817][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-11 20:44:51.818][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-11 20:44:51.819][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-11 20:44:51.820][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-11 20:44:51.821][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-11 20:44:51.822][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-11 20:44:51.825][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:51.826][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:51.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:51.832][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:51.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:51.833][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:51.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-11 20:44:51.835][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2024-09-11 20:44:51.838][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-11 20:44:51.839][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-11 20:44:51.840][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2024-09-11 20:44:52.800][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2024-09-11 20:44:54.020][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-11 20:44:54.023][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2024-09-11 20:44:54.027][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2024-09-11 20:44:54.030][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2024-09-11 20:44:54.031][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-11 20:44:54.033][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-11 20:44:54.034][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-11 20:44:54.036][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-11 20:44:54.037][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:54.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:54.042][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:54.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:54.044][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:54.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-11 20:44:54.049][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:54.050][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:54.051][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:54.052][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:54.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:54.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:54.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:54.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:54.058][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:54.059][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:54.060][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:54.061][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:54.063][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-11 20:44:54.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-11 20:44:54.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:54.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:54.067][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:54.068][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:54.069][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:54.070][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:54.071][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-11 20:44:54.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-11 20:44:54.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:54.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:54.075][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-11 20:44:54.076][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-11 20:44:54.077][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:54.078][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:54.079][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-11 20:44:54.080][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-11 20:44:54.081][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:54.082][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:54.084][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:54.085][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:54.086][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:54.087][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:54.088][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:54.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-11 20:44:54.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:54.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:54.092][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:54.093][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:54.094][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:54.095][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:54.096][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-11 20:44:54.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-11 20:44:54.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:54.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:54.100][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:54.101][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:54.102][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:54.103][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:54.104][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:54.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-11 20:44:54.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:54.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:54.108][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:54.109][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:54.110][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:54.111][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:54.113][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-11 20:44:54.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-11 20:44:54.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:54.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:54.117][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:54.118][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:54.119][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:54.120][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:54.121][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-11 20:44:54.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-11 20:44:54.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:54.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:54.125][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:54.126][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:54.127][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:54.128][ef$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:54.129][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-11 20:44:54.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-11 20:44:54.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:54.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:54.133][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:54.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:54.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:54.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:54.137][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:54.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:54.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:54.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:54.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:54.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:54.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:54.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:54.145][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-11 20:44:54.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-11 20:44:54.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:54.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:54.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:54.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:54.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:54.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:54.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:54.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:54.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:54.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:54.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:54.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:54.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:54.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:54.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:54.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:54.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:54.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:54.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:54.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:54.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:54.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-11 20:44:54.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-11 20:44:54.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-11 20:44:54.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-11 20:44:54.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-11 20:44:54.171][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-09-11 20:44:54.174][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-09-11 20:44:54.175][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-09-11 20:44:54.176][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-09-11 20:44:54.177][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-09-11 20:44:54.178][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-11 20:44:54.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-11 20:44:54.179][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-11 20:44:54.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-11 20:44:54.181][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-09-11 20:44:54.182][FUN] Functions in observer 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 379 ]
> 
> proc.time()
   user  system elapsed 
 22.173   0.609  51.700

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

nameusersystemelapsed
ChebiConn0.9260.0712.311
ChebiEntry0.1370.0000.136