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This page was generated on 2025-04-17 11:46 -0400 (Thu, 17 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4667
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4573
lconwaymacOS 12.7.1 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4599
kjohnson3macOS 13.7.1 Venturaarm644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4553
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4570
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 206/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbChebi 1.14.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-04-16 13:40 -0400 (Wed, 16 Apr 2025)
git_url: https://git.bioconductor.org/packages/biodbChebi
git_branch: RELEASE_3_21
git_last_commit: b8d718f
git_last_commit_date: 2025-04-15 12:39:10 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows 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 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for biodbChebi on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: biodbChebi
Version: 1.14.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings biodbChebi_1.14.0.tar.gz
StartedAt: 2025-04-17 04:27:19 -0000 (Thu, 17 Apr 2025)
EndedAt: 2025-04-17 04:30:22 -0000 (Thu, 17 Apr 2025)
EllapsedTime: 182.9 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbChebi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings biodbChebi_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/biodbChebi.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.14.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
ChebiConn 1.177  0.057   7.368
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

biodbChebi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL biodbChebi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘biodbChebi’ ...
** this is package ‘biodbChebi’ version ‘1.14.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbChebi)

Tests output

biodbChebi.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 [2025-04-17 04:28:23.053][biodb::testContext]
biodb.INFO [2025-04-17 04:28:23.056][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-17 04:28:23.058][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-04-17 04:28:23.059][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-17 04:28:23.060][biodb::testContext]
biodb.INFO [2025-04-17 04:28:23.069][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-04-17 04:28:23.072][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-devel_2025-02-19/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-04-17 04:28:23.081][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-17 04:28:23.083][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-17 04:28:23.084][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-17 04:28:23.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:23.090][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-17 04:28:23.118][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-17 04:28:23.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:23.124][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-17 04:28:23.125][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-17 04:28:23.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:23.130][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-17 04:28:23.132][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-17 04:28:23.133][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-17 04:28:23.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:23.138][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-17 04:28:23.140][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-17 04:28:23.141][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-17 04:28:23.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:23.146][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-17 04:28:23.148][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-17 04:28:23.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.151][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[2025-04-17 04:28:23.153][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-17 04:28:23.154][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-17 04:28:23.156][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-17 04:28:23.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:23.161][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-17 04:28:23.162][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-17 04:28:23.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:23.167][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-17 04:28:23.169][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-17 04:28:23.170][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-17 04:28:23.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:23.175][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-17 04:28:23.177][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-17 04:28:23.178][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-17 04:28:23.179][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-17 04:28:23.181][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-17 04:28:23.182][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-17 04:28:23.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.186][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[2025-04-17 04:28:23.187][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-17 04:28:23.189][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-17 04:28:23.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:23.194][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-17 04:28:23.195][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-17 04:28:23.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:23.201][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-17 04:28:23.202][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-17 04:28:23.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:23.207][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-17 04:28:23.209][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-17 04:28:23.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:23.214][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-17 04:28:23.216][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-17 04:28:23.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:23.222][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-17 04:28:23.223][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-17 04:28:23.229][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-17 04:28:23.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.233][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[2025-04-17 04:28:23.235][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-17 04:28:23.236][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-17 04:28:23.238][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-17 04:28:23.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:23.247][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-17 04:28:23.299][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-17 04:28:23.325][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-04-17 04:28:23.327][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-17 04:28:23.329][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-17 04:28:23.330][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-17 04:28:23.344][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-17 04:28:23.346][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-17 04:28:23.347][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-17 04:28:23.349][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-17 04:28:23.350][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-17 04:28:23.352][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-17 04:28:23.354][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-17 04:28:23.355][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-17 04:28:23.357][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:28:23.358][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-17 04:28:23.360][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-17 04:28:23.360][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-17 04:28:23.360][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-17 04:28:23.360][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-17 04:28:23.360][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-17 04:28:23.362][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-17 04:28:23.363][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:28:23.365][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:28:23.366][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-17 04:28:23.368][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:28:23.369][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:28:23.371][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-17 04:28:23.372][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:28:23.374][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-17 04:28:23.375][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-17 04:28:23.377][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-17 04:28:23.378][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:28:23.380][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-17 04:28:23.383][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-17 04:28:23.385][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-17 04:28:23.386][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-17 04:28:23.388][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-17 04:28:23.389][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-17 04:28:23.391][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-17 04:28:23.392][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-17 04:28:23.394][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-17 04:28:23.395][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-17 04:28:23.397][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-17 04:28:23.399][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-17 04:28:23.400][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-17 04:28:23.402][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-17 04:28:23.403][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:28:23.405][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-17 04:28:23.406][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-17 04:28:23.406][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-17 04:28:23.406][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-17 04:28:23.406][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-17 04:28:23.406][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-17 04:28:23.408][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-17 04:28:23.409][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:28:23.411][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:28:23.412][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-17 04:28:23.414][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:28:23.415][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:28:23.417][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-17 04:28:23.418][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:28:23.420][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-17 04:28:23.421][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-17 04:28:23.422][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-17 04:28:23.424][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:28:23.426][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-17 04:28:23.429][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-17 04:28:23.430][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-04-17 04:28:23.432][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-17 04:28:23.433][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-17 04:28:23.435][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-17 04:28:23.436][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-17 04:28:23.438][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-17 04:28:23.439][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-17 04:28:23.441][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-17 04:28:23.442][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-17 04:28:23.444][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-17 04:28:23.445][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-17 04:28:23.446][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-17 04:28:23.448][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:28:23.449][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-17 04:28:23.451][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:28:23.452][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-17 04:28:23.454][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:28:23.455][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:28:23.457][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-17 04:28:23.458][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:28:23.459][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:28:23.461][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-17 04:28:23.462][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:28:23.463][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-17 04:28:23.465][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-17 04:28:23.466][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-17 04:28:23.468][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:28:23.470][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-17 04:28:23.472][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-17 04:28:23.474][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-17 04:28:23.475][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-17 04:28:23.476][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-17 04:28:23.478][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-17 04:28:23.479][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-17 04:28:23.481][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-17 04:28:23.482][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-17 04:28:23.483][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-17 04:28:23.485][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-17 04:28:23.486][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-17 04:28:23.487][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-17 04:28:23.489][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-17 04:28:23.490][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:28:23.492][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-17 04:28:23.493][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:28:23.494][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-17 04:28:23.496][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:28:23.497][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:28:23.498][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-17 04:28:23.500][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:28:23.501][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:28:23.502][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-17 04:28:23.503][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:28:23.505][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-17 04:28:23.506][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-17 04:28:23.507][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-17 04:28:23.508][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:28:23.514][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-17 04:28:23.515][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.516][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.DEBUG[2025-04-17 04:28:23.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:23.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:23.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:23.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:23.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:23.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:23.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:23.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:23.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:23.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:23.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:23.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:23.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:23.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:23.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.546][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[2025-04-17 04:28:23.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:23.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:23.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.552][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[2025-04-17 04:28:23.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:23.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:23.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:23.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:23.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:23.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.564][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[2025-04-17 04:28:23.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:23.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:23.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.570][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[2025-04-17 04:28:23.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:23.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:23.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:23.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:23.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:23.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:23.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:23.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:23.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:23.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:23.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:23.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.594][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[2025-04-17 04:28:23.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:23.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:23.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:23.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:23.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:23.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:23.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:23.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:23.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.614][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.DEBUG[2025-04-17 04:28:23.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:23.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:23.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:23.622][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-17 04:28:23.628][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-17 04:28:23.630][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-17 04:28:23.632][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-17 04:28:23.635][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-17 04:28:23.637][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-17 04:28:23.639][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-17 04:28:23.641][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-17 04:28:23.643][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-17 04:28:23.645][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-17 04:28:23.647][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-17 04:28:23.649][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-17 04:28:23.651][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-17 04:28:23.653][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-17 04:28:23.655][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-17 04:28:23.658][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-17 04:28:23.660][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-17 04:28:23.662][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-17 04:28:23.664][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-17 04:28:23.666][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-17 04:28:23.668][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-17 04:28:23.670][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-17 04:28:23.672][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-17 04:28:23.675][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-17 04:28:23.677][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-17 04:28:23.679][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-17 04:28:23.681][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-17 04:28:23.683][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-17 04:28:23.685][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-17 04:28:23.687][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-17 04:28:23.690][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-17 04:28:23.692][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-17 04:28:23.694][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-17 04:28:23.696][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-17 04:28:23.698][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-17 04:28:23.700][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-17 04:28:23.703][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-17 04:28:23.705][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-17 04:28:23.707][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-17 04:28:23.709][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-17 04:28:23.711][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-17 04:28:23.713][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-17 04:28:23.716][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-17 04:28:23.718][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-17 04:28:23.720][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-17 04:28:23.722][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-17 04:28:23.724][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-17 04:28:23.726][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-17 04:28:23.728][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-17 04:28:23.739][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-17 04:28:23.742][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-17 04:28:23.744][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-17 04:28:23.746][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-17 04:28:23.748][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-17 04:28:23.750][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-17 04:28:23.753][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-17 04:28:23.755][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-17 04:28:23.757][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-17 04:28:23.760][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-17 04:28:23.762][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-17 04:28:23.764][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-17 04:28:23.767][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-17 04:28:23.769][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-17 04:28:23.771][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-17 04:28:23.774][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-17 04:28:23.776][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-17 04:28:23.778][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-17 04:28:23.781][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-17 04:28:23.783][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-17 04:28:23.785][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-17 04:28:23.788][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-17 04:28:23.790][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-17 04:28:23.792][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-17 04:28:23.795][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-17 04:28:23.797][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-17 04:28:23.799][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-17 04:28:23.802][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-17 04:28:23.804][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-17 04:28:23.806][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-17 04:28:23.808][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-17 04:28:23.811][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-17 04:28:23.813][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-17 04:28:23.815][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-17 04:28:23.824][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-17 04:28:23.827][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-04-17 04:28:23.831][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-17 04:28:23.832][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:23.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:23.835][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.836][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[2025-04-17 04:28:23.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:23.847][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:23.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:23.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:23.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.852][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.DEBUG[2025-04-17 04:28:23.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:23.856][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:23.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:23.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:23.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:23.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:23.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:23.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:23.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:23.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:23.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:23.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:23.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:23.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:23.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:23.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:23.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:23.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:23.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:23.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:23.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:23.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:23.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:23.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:23.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:23.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:23.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:23.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:23.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:23.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:23.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:23.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:23.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:23.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:23.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.913][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[2025-04-17 04:28:23.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:23.917][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:23.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:23.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:23.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.921][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[2025-04-17 04:28:23.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:23.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:23.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:23.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:23.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:23.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:23.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:23.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:23.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:23.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:23.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:23.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:23.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:23.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:23.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:23.948][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:23.950][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:23.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:23.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:23.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.955][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[2025-04-17 04:28:23.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:23.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:23.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:23.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:23.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:23.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:23.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:23.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:23.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:23.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:23.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:23.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:23.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:23.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:23.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:23.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:28:23.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:23.983][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:23.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:23.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:23.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:23.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:23.990][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-devel_2025-02-19/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-04-17 04:28:24.004][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-04-17 04:28:24.007][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-17 04:28:24.008][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-04-17 04:28:24.010][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-17 04:28:24.011][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-17 04:28:24.012][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-17 04:28:24.014][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-17 04:28:24.015][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-17 04:28:24.016][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-04-17 04:28:24.018][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-17 04:28:24.019][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-17 04:28:24.020][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-17 04:28:24.022][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-04-17 04:28:24.023][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-17 04:28:24.024][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-04-17 04:28:24.024][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-04-17 04:28:24.024][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-04-17 04:28:24.024][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-04-17 04:28:24.024][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-04-17 04:28:24.024][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-04-17 04:28:24.024][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-04-17 04:28:24.024][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-04-17 04:28:24.024][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-04-17 04:28:24.024][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-04-17 04:28:24.024][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-04-17 04:28:24.026][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-17 04:28:24.027][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-17 04:28:24.027][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-17 04:28:24.027][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-17 04:28:24.028][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-17 04:28:24.030][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:28:24.031][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:28:24.032][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-17 04:28:24.033][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:28:24.035][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:28:24.036][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-17 04:28:24.037][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-17 04:28:24.037][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-04-17 04:28:24.039][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-17 04:28:24.040][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-17 04:28:24.041][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-17 04:28:24.042][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-04-17 04:28:24.042][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-04-17 04:28:24.051][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-17 04:28:24.053][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-17 04:28:24.055][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-04-17 04:28:24.057][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-17 04:28:24.059][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-17 04:28:24.062][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-17 04:28:24.092][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-04-17 04:28:24.094][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-04-17 04:28:24.100][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-04-17 04:28:24.105][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-04-17 04:28:24.111][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-17 04:28:24.112][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-17 04:28:24.114][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-04-17 04:28:24.115][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-04-17 04:28:24.138][biodb::testThat]
biodb.INFO [2025-04-17 04:28:24.139][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-04-17 04:28:24.141][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-17 04:28:24.142][biodb::testThat]
biodb.TRACE[2025-04-17 04:28:24.147][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/R/R-devel_2025-02-19/site-library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2025-04-17 04:28:24.150][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-17 04:28:24.154][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-17 04:28:24.165][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:28:24.166][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:24.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:24.185][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:24.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:24.187][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:24.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:28:24.201][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:24.202][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:24.204][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.205][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.207][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:24.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:24.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.230][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:28:24.232][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:28:24.233][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.234][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.273][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:28:24.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:28:24.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.279][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:28:24.280][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:28:24.281][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.282][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.284][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:28:24.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:28:24.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.290][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:28:24.292][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:28:24.293][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.294][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.296][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:28:24.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:28:24.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.302][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:28:24.303][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:28:24.305][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.306][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.308][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:28:24.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:28:24.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.313][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:24.315][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:24.316][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.317][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.319][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:24.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:24.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.325][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:28:24.327][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:24.328][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.329][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.331][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:28:24.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:24.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.337][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:24.339][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:24.340][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.342][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.344][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:24.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:24.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.349][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:28:24.351][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:28:24.352][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.354][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.356][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:28:24.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:28:24.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.362][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:28:24.363][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:28:24.365][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.366][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.368][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:28:24.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:28:24.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.374][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:28:24.376][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:28:24.377][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.379][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.380][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:28:24.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:28:24.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.386][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:24.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:24.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.392][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:24.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:24.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:24.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:24.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.404][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:24.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:24.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:24.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:24.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:24.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:24.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:24.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:24.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:24.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:24.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:24.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:24.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:24.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:24.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:28:24.527][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-04-17 04:28:24.530][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:28:24.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:28:24.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.536][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:28:24.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:28:24.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.577][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:28:24.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:28:24.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.582][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:28:24.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:28:24.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.588][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:24.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:24.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.593][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:24.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:24.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.599][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-17 04:28:24.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-17 04:28:24.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.604][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-17 04:28:24.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-17 04:28:24.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.610][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-17 04:28:24.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-17 04:28:24.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.615][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-17 04:28:24.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-17 04:28:24.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:24.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:24.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.665][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:24.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:24.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:24.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:24.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:24.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:24.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:24.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:24.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:24.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:24.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:24.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:24.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:24.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:24.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.712][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:24.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:24.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.717][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:24.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:24.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.723][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:24.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:24.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:24.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:24.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:24.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:24.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.750][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:24.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:24.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.756][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:24.757][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:24.759][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.760][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:24.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:24.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.779][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:24.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:24.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.785][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:24.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:24.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.791][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:24.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:24.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.797][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:24.798][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:24.799][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.801][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.802][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:24.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:24.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.819][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:28:24.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:28:24.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.834][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:28:24.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:28:24.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.840][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:28:24.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:28:24.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.846][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:28:24.847][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:28:24.849][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.850][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.852][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:28:24.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:28:24.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.869][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:28:24.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:28:24.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.875][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:28:24.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:28:24.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.882][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:28:24.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:28:24.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.888][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:28:24.890][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:28:24.891][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.893][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.894][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:28:24.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:28:24.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.911][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:24.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:24.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.917][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:24.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:24.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.922][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:24.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:24.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.928][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:24.930][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:24.931][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.932][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.934][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:24.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:24.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.950][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:24.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:24.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.956][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:24.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:24.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.962][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:24.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:24.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.967][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:24.969][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:24.970][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.972][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.973][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:24.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:24.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.990][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:28:24.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:28:24.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:24.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:24.995][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:28:24.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:28:24.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.001][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:28:25.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:28:25.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.007][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:28:25.008][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:28:25.010][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.011][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.012][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:28:25.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:28:25.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.029][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-04-17 04:28:25.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:28:25.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.035][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-04-17 04:28:25.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:28:25.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.040][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-04-17 04:28:25.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:28:25.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.046][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-04-17 04:28:25.048][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:28:25.049][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.050][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.052][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-04-17 04:28:25.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:28:25.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.068][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:25.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:25.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.073][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:25.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:25.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.079][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:25.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:25.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.084][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:25.086][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:25.087][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.088][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.090][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:25.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:25.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.106][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:28:25.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:28:25.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.111][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:28:25.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:28:25.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.117][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:28:25.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:28:25.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.122][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:28:25.124][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:28:25.125][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.126][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.128][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:28:25.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:28:25.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.145][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:28:25.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:28:25.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.150][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:28:25.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:28:25.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.156][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:28:25.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:28:25.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.162][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:28:25.172][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:28:25.174][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.175][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.177][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:28:25.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:28:25.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.195][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:28:25.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:28:25.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.201][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:28:25.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:28:25.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.207][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:28:25.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:28:25.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.214][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:28:25.216][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:28:25.218][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.219][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.221][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:28:25.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:28:25.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.238][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:25.239][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:25.241][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.242][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.249][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:28:25.251][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:28:25.253][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.254][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.262][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:28:25.263][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:28:25.265][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.266][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.273][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:28:25.275][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:28:25.276][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.277][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.284][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:28:25.286][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:28:25.287][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.288][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.295][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:25.297][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:25.298][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.299][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.306][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:25.308][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:25.309][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.311][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.317][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:25.319][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:25.320][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.322][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.328][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-04-17 04:28:25.330][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:28:25.331][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.333][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.339][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:28:25.341][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:28:25.342][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.344][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.350][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:28:25.352][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:28:25.353][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.355][ef$get] fields variable is a list.
biodb.INFO [2025-04-17 04:28:25.365][biodb::testThat]
biodb.INFO [2025-04-17 04:28:25.367][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-04-17 04:28:25.368][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-17 04:28:25.369][biodb::testThat]
biodb.DEBUG[2025-04-17 04:28:25.390][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-04-17 04:28:25.399][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-17 04:28:25.405][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2025-04-17 04:28:25.406][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-17 04:28:25.408][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2025-04-17 04:28:25.410][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-17 04:28:25.445][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-17 04:28:25.447][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-17 04:28:25.449][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:28:25.450][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:25.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:25.457][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:25.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:25.460][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:25.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:28:25.464][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:25.466][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:25.467][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.468][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:25.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:25.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.509][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:28:25.510][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:28:25.512][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.513][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.515][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:28:25.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:28:25.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.521][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:28:25.522][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:28:25.524][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.525][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.527][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:28:25.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:28:25.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.533][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:28:25.534][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:28:25.536][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.537][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.539][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:28:25.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:28:25.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.545][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:28:25.546][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:28:25.548][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.549][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.551][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:28:25.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:28:25.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.556][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:25.558][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:25.559][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.560][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.562][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:25.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:25.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.568][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:28:25.569][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:25.570][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.572][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.573][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:28:25.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:25.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.579][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:25.580][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:25.582][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.583][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.585][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:25.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:25.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.590][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:28:25.592][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:28:25.593][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.594][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.596][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:28:25.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:28:25.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.602][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:28:25.603][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:28:25.605][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.606][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.608][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:28:25.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:28:25.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.613][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:28:25.615][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:28:25.616][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.617][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.619][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:28:25.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:28:25.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.624][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:25.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:25.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.630][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:25.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:25.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:25.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:25.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.640][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:25.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:25.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:25.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:25.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:25.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:25.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:25.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:25.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:25.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:25.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:25.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:25.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:25.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:25.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:28:25.677][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2025-04-17 04:28:25.679][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-04-17 04:28:25.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-04-17 04:28:25.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.684][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-04-17 04:28:25.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-04-17 04:28:25.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.689][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-04-17 04:28:25.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-04-17 04:28:25.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-17 04:28:25.704][biodb::testThat]
biodb.INFO [2025-04-17 04:28:25.705][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-04-17 04:28:25.706][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-17 04:28:25.708][biodb::testThat]
biodb.TRACE[2025-04-17 04:28:25.712][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:28:25.713][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:28:25.714][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.716][ef$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:28:25.717][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2025-04-17 04:28:25.753][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:28:25.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:28:25.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.759][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:28:25.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:28:25.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.764][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:28:25.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:28:25.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:28:25.773][function(conn, opt)] With value "squalene".
biodb.DEBUG[2025-04-17 04:28:25.779][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-04-17 04:28:25.818][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-17 04:28:25.842][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-04-17 04:28:25.844][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-17 04:28:25.846][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-04-17 04:28:25.881][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[2025-04-17 04:28:25.886][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-17 04:28:25.888][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-17 04:28:25.889][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-17 04:28:25.892][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-04-17 04:28:25.895][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2025-04-17 04:28:25.910][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:25.912][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:25.913][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.914][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.916][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:25.917][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:25.919][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.920][ef$get] fields variable is a list.
biodb.INFO [2025-04-17 04:28:25.925][biodb::testThat]
biodb.INFO [2025-04-17 04:28:25.927][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-04-17 04:28:25.928][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-17 04:28:25.929][biodb::testThat]
biodb.TRACE[2025-04-17 04:28:25.963][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:28:25.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:28:25.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.969][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:28:25.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:28:25.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:25.974][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:28:25.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:28:25.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:25.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:28:26.057][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[2025-04-17 04:28:26.062][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-17 04:28:26.064][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-17 04:28:26.065][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-17 04:28:26.067][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2025-04-17 04:28:26.088][biodb::testThat]
biodb.INFO [2025-04-17 04:28:26.090][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-04-17 04:28:26.091][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-17 04:28:26.092][biodb::testThat]
biodb.TRACE[2025-04-17 04:28:26.132][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:28:26.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:28:26.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:26.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:26.138][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:28:26.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:28:26.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:26.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:26.143][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:28:26.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:28:26.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:26.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:26.149][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:28:26.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:28:26.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:26.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:26.155][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:26.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:26.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:26.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:26.161][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:26.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:26.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:26.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:26.166][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-17 04:28:26.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-17 04:28:26.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:26.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:26.171][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-17 04:28:26.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-17 04:28:26.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:26.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:26.177][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-17 04:28:26.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-17 04:28:26.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:26.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:26.182][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-17 04:28:26.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-17 04:28:26.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:26.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:26.213][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:28:26.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:28:26.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:26.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:26.218][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:28:26.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:28:26.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:26.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:26.224][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:28:26.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:28:26.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:26.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:26.229][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:28:26.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:28:26.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:26.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:26.235][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:26.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:26.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:26.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:26.241][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:26.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:26.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:26.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:26.246][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-17 04:28:26.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-17 04:28:26.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:26.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:26.252][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-17 04:28:26.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-17 04:28:26.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:26.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:26.257][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-17 04:28:26.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-17 04:28:26.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:26.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:26.263][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-17 04:28:26.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-17 04:28:26.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:26.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-17 04:28:26.276][biodb::testThat]
biodb.INFO [2025-04-17 04:28:26.277][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-04-17 04:28:26.278][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-17 04:28:26.280][biodb::testThat]
biodb.INFO [2025-04-17 04:28:26.291][biodb::testThat]
biodb.INFO [2025-04-17 04:28:26.293][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-04-17 04:28:26.294][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-17 04:28:26.295][biodb::testThat]
biodb.INFO [2025-04-17 04:28:26.307][biodb::testThat]
biodb.INFO [2025-04-17 04:28:26.309][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-04-17 04:28:26.310][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-17 04:28:26.311][biodb::testThat]
biodb.DEBUG[2025-04-17 04:28:26.317][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2025-04-17 04:28:27.616][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2025-04-17 04:28:29.833][biodb::testThat]
biodb.INFO [2025-04-17 04:28:29.835][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-04-17 04:28:29.836][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-17 04:28:29.838][biodb::testThat]
biodb.DEBUG[2025-04-17 04:28:39.488][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[2025-04-17 04:28:40.979][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:28:40.983][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:28:40.985][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:40.988][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:40.990][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:40.992][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:40.995][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:40.997][ef$get] fields variable is a list.
biodb.INFO [2025-04-17 04:28:41.001][biodb::testThat]
biodb.INFO [2025-04-17 04:28:41.003][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2025-04-17 04:28:41.006][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-17 04:28:41.008][biodb::testThat]
biodb.TRACE[2025-04-17 04:28:41.031][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:28:41.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:28:41.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:41.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:41.039][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:28:41.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:28:41.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:41.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:41.048][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:28:41.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:28:41.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:41.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:28:41.221][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[2025-04-17 04:28:41.228][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-17 04:28:41.230][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-17 04:28:41.233][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-17 04:28:41.236][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-04-17 04:28:41.385][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[2025-04-17 04:28:41.389][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-17 04:28:41.392][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-17 04:28:41.394][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-17 04:28:41.395][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2025-04-17 04:28:41.416][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-17 04:28:41.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-17 04:28:41.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:41.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:41.427][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:41.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:41.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:41.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:41.434][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:41.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:41.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:41.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:41.441][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:41.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:41.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:41.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:41.446][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:41.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:41.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:41.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:41.452][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:41.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:41.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:41.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:28:41.468][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[2025-04-17 04:28:41.473][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-17 04:28:41.475][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-04-17 04:28:41.477][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-17 04:28:41.480][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-04-17 04:28:41.483][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:28:41.485][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:41.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:41.493][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:41.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:41.496][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:41.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:41.499][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2025-04-17 04:28:41.581][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-17 04:28:41.584][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2025-04-17 04:28:41.586][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-17 04:28:41.587][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-17 04:28:41.589][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-17 04:28:41.591][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-17 04:28:41.592][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-17 04:28:41.593][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-17 04:28:41.597][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:28:41.599][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:41.600][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:41.607][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:41.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:41.609][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:41.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:41.612][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2025-04-17 04:28:41.617][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:28:41.618][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:28:41.620][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2025-04-17 04:28:42.727][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2025-04-17 04:28:43.484][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:28:43.487][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2025-04-17 04:28:43.508][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2025-04-17 04:28:43.512][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2025-04-17 04:28:43.515][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-17 04:28:43.517][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-17 04:28:43.518][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-17 04:28:43.521][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:28:43.522][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:43.523][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:43.530][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:43.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:43.533][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:43.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:28:43.538][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:43.540][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:43.541][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:43.542][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:43.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:43.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:43.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:43.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:43.550][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:28:43.551][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:28:43.553][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:43.554][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:43.556][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:28:43.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:28:43.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:43.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:43.561][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:28:43.563][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:28:43.564][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:43.565][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:43.568][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:28:43.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:28:43.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:43.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:43.574][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:28:43.575][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:28:43.576][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:43.578][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:43.579][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:28:43.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:28:43.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:43.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:43.585][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:28:43.587][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:28:43.588][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:43.589][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:43.591][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:28:43.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:28:43.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:43.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:43.597][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:43.598][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:43.599][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:43.601][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:43.602][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:28:43.604][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:43.605][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:43.606][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:43.608][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:28:43.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:43.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:43.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:43.614][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:43.615][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:43.616][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:43.618][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:43.619][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:43.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:43.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:43.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:43.625][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:28:43.626][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:28:43.628][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:43.629][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:43.631][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:28:43.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:28:43.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:43.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:43.636][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:28:43.638][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:28:43.639][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:43.640][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:43.642][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:28:43.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:28:43.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:43.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:43.648][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:28:43.649][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:28:43.650][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:43.652][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:43.653][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:28:43.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:28:43.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:43.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:43.659][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:43.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:43.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:43.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:43.664][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:43.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:43.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:43.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:43.670][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:43.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:43.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:43.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:43.689][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:43.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:43.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:43.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:43.694][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:43.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:43.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:43.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:43.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:43.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:43.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:43.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:43.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:43.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:43.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:43.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:43.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:43.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:43.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:43.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:43.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:43.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:43.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:43.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:43.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:43.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:43.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:43.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:28:43.728][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2025-04-17 04:28:43.742][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:43.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:43.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:43.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:43.748][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:43.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:43.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:43.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:43.753][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:43.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:43.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:43.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:28:43.760][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[2025-04-17 04:28:43.765][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-17 04:28:43.767][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-04-17 04:28:43.768][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-17 04:28:43.771][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-04-17 04:28:43.795][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:28:43.797][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:43.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:43.804][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:43.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:43.807][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:43.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:28:43.810][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:43.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:43.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:43.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:43.815][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:43.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:43.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:43.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:43.821][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:43.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:43.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:43.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:28:43.826][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:28:43.827][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:43.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:43.835][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:43.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:43.838][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:43.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:43.841][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2025-04-17 04:28:43.842][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-17 04:28:43.844][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2025-04-17 04:28:43.846][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-17 04:28:43.847][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-17 04:28:43.849][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-17 04:28:43.850][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-17 04:28:43.851][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-17 04:28:43.853][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-17 04:28:43.874][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:28:43.875][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:43.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:43.884][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:43.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:43.886][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:43.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:43.889][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2025-04-17 04:28:43.913][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:28:43.914][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:28:43.948][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2025-04-17 04:28:46.956][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2025-04-17 04:28:47.685][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:28:47.688][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2025-04-17 04:28:47.692][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2025-04-17 04:28:47.696][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2025-04-17 04:28:47.698][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-17 04:28:47.700][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-17 04:28:47.701][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-17 04:28:47.704][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:28:47.705][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:47.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:47.713][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:47.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:47.716][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:47.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:28:47.720][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:47.722][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:47.723][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:47.724][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:47.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:47.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:47.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:47.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:47.731][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:28:47.733][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:28:47.734][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:47.735][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:47.737][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:28:47.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:28:47.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:47.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:47.743][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:28:47.744][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:28:47.746][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:47.747][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:47.749][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:28:47.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:28:47.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:47.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:47.754][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:28:47.756][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:28:47.757][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:47.758][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:47.760][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:28:47.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:28:47.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:47.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:47.766][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:28:47.767][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:28:47.768][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:47.770][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:47.771][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:28:47.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:28:47.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:47.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:47.777][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:47.778][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:47.780][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:47.781][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:47.783][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:28:47.784][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:47.785][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:47.787][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:47.788][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:28:47.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:47.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:47.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:47.794][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:47.796][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:47.797][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:47.798][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:47.800][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:47.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:47.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:47.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:47.805][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:28:47.807][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:28:47.808][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:47.809][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:47.811][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:28:47.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:28:47.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:47.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:47.817][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:28:47.818][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:28:47.820][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:47.821][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:47.823][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:28:47.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:28:47.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:47.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:47.828][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:28:47.830][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:28:47.831][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:47.832][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:47.834][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:28:47.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:28:47.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:47.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:47.840][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:47.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:47.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:47.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:47.846][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:47.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:47.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:47.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:47.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:47.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:47.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:47.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:47.857][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:47.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:47.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:47.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:47.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:47.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:47.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:47.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:47.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:47.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:47.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:47.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:47.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:47.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:47.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:47.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:47.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:47.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:47.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:47.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:47.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:47.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:47.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:47.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:47.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:47.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:47.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:47.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:28:47.895][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2025-04-17 04:28:47.896][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:47.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:47.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:47.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:47.902][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:47.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:47.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:47.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:47.907][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:47.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:47.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:47.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:28:47.951][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[2025-04-17 04:28:47.955][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-17 04:28:47.957][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-17 04:28:47.959][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-17 04:28:47.961][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-04-17 04:28:47.965][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:28:47.966][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:47.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:47.974][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:47.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:47.977][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:47.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:28:47.980][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:47.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:47.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:47.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:47.986][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:47.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:47.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:47.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:47.991][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:47.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:47.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:47.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:28:47.997][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:28:47.998][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:48.000][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:48.006][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:48.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:48.009][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:48.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:48.012][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2025-04-17 04:28:48.013][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-17 04:28:48.015][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2025-04-17 04:28:48.017][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-17 04:28:48.019][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-17 04:28:48.020][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-17 04:28:48.021][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-17 04:28:48.023][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-17 04:28:48.024][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-17 04:28:48.028][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:28:48.029][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:48.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:48.037][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:48.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:48.040][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:48.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:48.043][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2025-04-17 04:28:48.047][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:28:48.048][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:28:48.049][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2025-04-17 04:28:48.834][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2025-04-17 04:28:49.648][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:28:49.650][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2025-04-17 04:28:49.655][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2025-04-17 04:28:49.658][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2025-04-17 04:28:49.660][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-17 04:28:49.662][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-17 04:28:49.663][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-17 04:28:49.666][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:28:49.667][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:49.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:49.674][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:49.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:49.677][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:49.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:28:49.681][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:49.683][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:49.684][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:49.685][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:49.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:49.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:49.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:49.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:49.693][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:28:49.694][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:28:49.695][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:49.697][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:49.698][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:28:49.700][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:28:49.701][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:49.703][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:49.704][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:28:49.706][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:28:49.707][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:49.709][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:49.710][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:28:49.712][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:28:49.713][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:49.715][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:49.716][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:49.718][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:49.719][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:49.720][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:49.722][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:28:49.724][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:49.725][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:49.726][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:49.728][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:49.729][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:49.731][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:49.732][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:49.734][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:28:49.735][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:28:49.737][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:49.738][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:49.740][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:28:49.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:28:49.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:49.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:49.746][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:28:49.748][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:28:49.749][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:49.750][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:49.752][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:28:49.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:28:49.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:49.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:49.758][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:28:49.759][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:28:49.761][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:49.762][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:49.764][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:49.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:49.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:49.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:49.770][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:49.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:49.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:49.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:49.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:49.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:49.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:49.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:49.794][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:49.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:49.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:49.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:49.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:49.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:49.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:49.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:49.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:49.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:49.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:49.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:49.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:49.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:49.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:49.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:49.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:49.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:49.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:49.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:49.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:49.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:49.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:49.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:49.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:49.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:49.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:49.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:28:49.834][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2025-04-17 04:28:49.836][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:49.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:49.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:49.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:49.842][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:49.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:49.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:49.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:49.847][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:49.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:49.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:49.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:49.853][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:49.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:49.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:49.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:49.859][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:49.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:49.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:49.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:28:49.865][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:28:49.867][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:49.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:49.875][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:49.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:49.878][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:49.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:49.881][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2025-04-17 04:28:49.882][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-17 04:28:49.884][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2025-04-17 04:28:49.886][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-17 04:28:49.888][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-17 04:28:49.890][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-17 04:28:49.891][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-17 04:28:49.893][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-17 04:28:49.894][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-17 04:28:49.898][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:28:49.899][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:49.901][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:49.907][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:49.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:49.910][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:49.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:49.913][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2025-04-17 04:28:49.917][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:28:49.919][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:28:49.921][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2025-04-17 04:28:50.685][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2025-04-17 04:28:51.463][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:28:51.466][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2025-04-17 04:28:51.471][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2025-04-17 04:28:51.474][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2025-04-17 04:28:51.477][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-17 04:28:51.478][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-17 04:28:51.480][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-17 04:28:51.482][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:28:51.484][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:51.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:51.492][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:51.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:51.495][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:51.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:28:51.499][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:51.501][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:51.502][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:51.503][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:51.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:51.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:51.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:51.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:51.511][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:28:51.512][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:28:51.514][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:51.515][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:51.517][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:28:51.518][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:28:51.520][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:51.521][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:51.523][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:28:51.524][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:28:51.526][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:51.527][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:51.529][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:28:51.530][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:28:51.532][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:51.533][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:51.535][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:51.536][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:51.538][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:51.539][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:51.541][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:28:51.542][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:51.544][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:51.545][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:51.547][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:51.548][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:51.550][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:51.551][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:51.553][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:28:51.554][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:28:51.555][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:51.557][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:51.559][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:28:51.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:28:51.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:51.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:51.565][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:28:51.566][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:28:51.568][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:51.569][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:51.571][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:28:51.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:28:51.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:51.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:51.577][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:28:51.578][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:28:51.579][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:51.581][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:51.583][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:51.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:51.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:51.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:51.588][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:51.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:51.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:51.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:51.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:51.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:51.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:51.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:51.613][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:51.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:51.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:51.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:51.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:51.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:51.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:51.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:51.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:51.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:51.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:51.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:51.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:51.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:51.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:51.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:51.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:51.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:51.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:51.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:51.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:51.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:51.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:51.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:51.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:51.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:51.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:51.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:28:51.657][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2025-04-17 04:28:51.659][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:51.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:51.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:51.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:51.665][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:51.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:51.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:51.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:51.671][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:51.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:51.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:51.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:51.678][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:51.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:51.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:51.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:51.698][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:51.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:51.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:51.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:28:51.712][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:28:51.714][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:51.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:51.735][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:51.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:51.739][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:51.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:51.744][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2025-04-17 04:28:51.747][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-17 04:28:51.752][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2025-04-17 04:28:51.755][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-17 04:28:51.757][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-17 04:28:51.760][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-17 04:28:51.762][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-17 04:28:51.765][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-17 04:28:51.767][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-17 04:28:51.775][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:28:51.777][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:51.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:51.789][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:51.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:51.793][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:51.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:51.798][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2025-04-17 04:28:51.804][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:28:51.807][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:28:51.810][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2025-04-17 04:28:52.666][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2025-04-17 04:28:53.475][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:28:53.478][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2025-04-17 04:28:53.483][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2025-04-17 04:28:53.487][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2025-04-17 04:28:53.489][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-17 04:28:53.491][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-17 04:28:53.493][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-17 04:28:53.496][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:28:53.498][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:53.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:53.507][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:53.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:53.510][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:53.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:28:53.516][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:53.518][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:53.519][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:53.521][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:53.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:53.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:53.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:53.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:53.529][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:28:53.531][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:28:53.532][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:53.534][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:53.536][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:28:53.537][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:28:53.539][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:53.540][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:53.543][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:28:53.544][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:28:53.546][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:53.547][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:53.549][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:28:53.551][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:28:53.552][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:53.554][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:53.555][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:53.557][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:53.559][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:53.560][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:53.562][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:28:53.563][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:53.565][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:53.566][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:53.568][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:53.570][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:53.571][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:53.573][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:53.575][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:28:53.576][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:28:53.578][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:53.579][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:53.582][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:28:53.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:28:53.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:53.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:53.589][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:28:53.591][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:28:53.592][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:53.593][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:53.595][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:28:53.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:28:53.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:53.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:53.601][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:28:53.603][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:28:53.604][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:53.606][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:53.608][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:53.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:53.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:53.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:53.634][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:53.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:53.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:53.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:53.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:53.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:53.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:53.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:53.646][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:53.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:53.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:53.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:53.653][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:53.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:53.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:53.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:53.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:53.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:53.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:53.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:53.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:53.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:53.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:53.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:53.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:53.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:53.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:53.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:53.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:53.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:53.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:53.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:53.684][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:53.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:53.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:53.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:28:53.690][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2025-04-17 04:28:53.691][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:53.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:53.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:53.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:53.698][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:53.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:53.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:53.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:53.704][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:53.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:53.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:53.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:53.710][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:53.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:53.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:53.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:53.715][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:53.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:53.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:53.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:28:53.721][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:28:53.722][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:53.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:53.730][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:53.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:53.733][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:53.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:53.736][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2025-04-17 04:28:53.737][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-17 04:28:53.740][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2025-04-17 04:28:53.741][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-17 04:28:53.743][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-17 04:28:53.745][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-17 04:28:53.746][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-17 04:28:53.748][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-17 04:28:53.749][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-17 04:28:53.753][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:28:53.754][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:53.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:53.763][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:53.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:53.765][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:53.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:53.768][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2025-04-17 04:28:53.772][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:28:53.774][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:28:53.776][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2025-04-17 04:28:54.528][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2025-04-17 04:28:55.316][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:28:55.319][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2025-04-17 04:28:55.324][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2025-04-17 04:28:55.327][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2025-04-17 04:28:55.329][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-17 04:28:55.331][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-17 04:28:55.332][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-17 04:28:55.335][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:28:55.336][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:55.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:55.344][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:55.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:55.347][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:55.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:28:55.351][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:55.353][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:55.354][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:55.355][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:55.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:55.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:55.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:55.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:55.363][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:28:55.364][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:28:55.366][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:55.367][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:55.369][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:28:55.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:28:55.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:55.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:55.374][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:28:55.376][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:28:55.377][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:55.379][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:55.381][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:28:55.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:28:55.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:55.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:55.387][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:28:55.388][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:28:55.389][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:55.391][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:55.393][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:28:55.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:28:55.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:55.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:55.398][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:28:55.400][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:28:55.401][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:55.402][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:55.404][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:28:55.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:28:55.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:55.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:55.410][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:55.412][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:55.413][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:55.415][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:55.416][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:55.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:55.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:55.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:55.423][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:28:55.424][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:55.426][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:55.427][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:55.441][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:28:55.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:55.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:55.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:55.447][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:55.449][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:55.450][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:55.451][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:55.453][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:55.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:55.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:55.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:55.459][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:28:55.461][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:28:55.462][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:55.463][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:55.466][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:28:55.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:28:55.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:55.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:55.472][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:28:55.473][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:28:55.475][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:55.476][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:55.478][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:28:55.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:28:55.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:55.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:55.484][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:28:55.486][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:28:55.487][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:55.488][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:55.490][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:28:55.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:28:55.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:55.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:55.496][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:55.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:55.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:55.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:55.502][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:55.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:55.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:55.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:55.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:55.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:55.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:55.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:55.514][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:55.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:55.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:55.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:55.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:55.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:55.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:55.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:55.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:55.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:55.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:55.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:55.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:55.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:55.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:55.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:55.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:55.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:55.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:55.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:55.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:55.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:55.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:55.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:55.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:55.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:55.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:55.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:28:55.554][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2025-04-17 04:28:55.555][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:55.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:55.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:55.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:55.561][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:55.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:55.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:55.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:55.567][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:55.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:55.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:55.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:28:55.572][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:28:55.573][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:55.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:55.582][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:55.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:55.584][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:55.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:55.587][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2025-04-17 04:28:55.588][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-17 04:28:55.591][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2025-04-17 04:28:55.593][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-17 04:28:55.594][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-17 04:28:55.596][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-17 04:28:55.598][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-17 04:28:55.599][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-17 04:28:55.601][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-17 04:28:55.605][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:28:55.606][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:55.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:55.614][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:55.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:55.617][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:55.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:55.620][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2025-04-17 04:28:55.624][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:28:55.625][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:28:55.627][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2025-04-17 04:28:56.378][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2025-04-17 04:28:57.200][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2025-04-17 04:28:57.202][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2025-04-17 04:28:57.204][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2025-04-17 04:28:57.209][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2025-04-17 04:28:57.212][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2025-04-17 04:28:57.214][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-17 04:28:57.216][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-17 04:28:57.217][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-17 04:28:57.219][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:28:57.221][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:57.222][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:57.228][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:57.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:57.231][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:57.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:28:57.235][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:57.237][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:57.238][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:57.239][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:57.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:57.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:57.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:57.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:57.246][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:28:57.248][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:28:57.249][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:57.250][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:57.252][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:28:57.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:28:57.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:57.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:57.257][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:28:57.259][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:28:57.260][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:57.261][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:57.263][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:28:57.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:28:57.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:57.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:57.281][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:28:57.282][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:28:57.284][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:57.285][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:57.287][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:28:57.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:28:57.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:57.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:57.292][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:28:57.293][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:28:57.295][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:57.296][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:57.298][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:28:57.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:28:57.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:57.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:57.303][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:57.304][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:57.306][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:57.307][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:57.309][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:57.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:57.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:57.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:57.314][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:28:57.315][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:57.317][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:57.318][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:57.320][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:28:57.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:57.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:57.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:57.325][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:57.326][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:57.328][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:57.329][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:57.331][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:57.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:57.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:57.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:57.336][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:28:57.338][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:28:57.339][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:57.340][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:57.342][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:28:57.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:28:57.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:57.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:57.347][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:28:57.349][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:28:57.350][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:57.351][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:57.353][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:28:57.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:28:57.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:57.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:57.359][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:28:57.360][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:28:57.361][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:57.363][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:57.364][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:28:57.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:28:57.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:57.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:57.370][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:57.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:57.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:57.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:57.375][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:57.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:57.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:57.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:57.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:57.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:57.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:57.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:57.386][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:57.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:57.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:57.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:57.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:57.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:57.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:57.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:57.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:57.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:57.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:57.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:57.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:57.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:57.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:57.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:57.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:57.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:57.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:57.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:57.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:57.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:57.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:57.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:57.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:57.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:57.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:57.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:28:57.425][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2025-04-17 04:28:57.427][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:57.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:57.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:57.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:57.432][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:57.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:57.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:57.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:57.437][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:57.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:57.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:57.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:28:57.442][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:28:57.443][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:57.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:57.451][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:57.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:57.454][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:57.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:57.456][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2025-04-17 04:28:57.457][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-17 04:28:57.460][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2025-04-17 04:28:57.461][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-17 04:28:57.463][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-17 04:28:57.464][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-17 04:28:57.465][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-17 04:28:57.467][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-17 04:28:57.468][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-17 04:28:57.472][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:28:57.483][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:57.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:57.505][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:57.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:57.509][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:57.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:57.514][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2025-04-17 04:28:57.522][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:28:57.524][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:28:57.527][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2025-04-17 04:28:58.290][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2025-04-17 04:28:59.106][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:28:59.110][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2025-04-17 04:28:59.115][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2025-04-17 04:28:59.119][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2025-04-17 04:28:59.121][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-17 04:28:59.123][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-17 04:28:59.125][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-17 04:28:59.129][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:28:59.131][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:59.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:59.163][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:59.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:59.166][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:59.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:28:59.171][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:59.173][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:59.174][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:59.176][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:59.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:59.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:59.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:59.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:59.184][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:28:59.186][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:28:59.188][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:59.189][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:59.191][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:28:59.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:28:59.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:59.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:59.198][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:28:59.200][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:28:59.201][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:59.203][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:59.205][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:28:59.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:28:59.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:59.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:59.211][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:28:59.213][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:28:59.214][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:59.216][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:59.217][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:28:59.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:28:59.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:59.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:59.224][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:28:59.225][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:28:59.227][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:59.228][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:59.230][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:28:59.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:28:59.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:59.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:59.237][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:59.238][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:28:59.240][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:59.242][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:59.244][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:28:59.246][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:59.248][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:59.249][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:59.252][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:28:59.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:59.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:59.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:59.260][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:59.262][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:59.264][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:59.265][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:59.268][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:59.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:28:59.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:59.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:59.276][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:28:59.278][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:28:59.280][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:59.281][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:59.285][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:28:59.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:28:59.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:59.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:59.293][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:28:59.295][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:28:59.297][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:59.298][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:59.301][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:28:59.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:28:59.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:59.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:59.309][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:28:59.311][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:28:59.313][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:59.314][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:59.317][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:28:59.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:28:59.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:59.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:59.324][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:59.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:59.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:59.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:59.331][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:59.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:59.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:59.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:59.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:59.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:59.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:59.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:59.343][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:28:59.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:28:59.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:59.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:59.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:59.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:59.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:59.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:59.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:59.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:59.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:59.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:59.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:59.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:59.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:59.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:59.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:59.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:59.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:59.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:59.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:59.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:59.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:59.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:59.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:28:59.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:28:59.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:59.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:28:59.386][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2025-04-17 04:28:59.388][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:59.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:59.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:59.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:59.394][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:59.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:59.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:59.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:28:59.400][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:59.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:28:59.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:28:59.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:28:59.405][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:28:59.407][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:59.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:59.414][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:59.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:59.417][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:59.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:59.420][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2025-04-17 04:28:59.421][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-17 04:28:59.424][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2025-04-17 04:28:59.425][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-17 04:28:59.427][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-17 04:28:59.429][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-17 04:28:59.430][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-17 04:28:59.432][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-17 04:28:59.433][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-17 04:28:59.437][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:28:59.438][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:28:59.440][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:28:59.446][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:28:59.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:28:59.449][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:28:59.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:28:59.461][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2025-04-17 04:28:59.465][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:28:59.466][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:28:59.468][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2025-04-17 04:29:00.309][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2025-04-17 04:29:01.115][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2025-04-17 04:29:01.118][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2025-04-17 04:29:01.120][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2025-04-17 04:29:01.124][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2025-04-17 04:29:01.128][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2025-04-17 04:29:01.129][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-17 04:29:01.131][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-17 04:29:01.133][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-17 04:29:01.135][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:01.136][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:01.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:01.144][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:01.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:01.147][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:01.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:01.151][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:01.153][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:01.154][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:01.155][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:01.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:01.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:01.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:01.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:01.163][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:29:01.164][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:29:01.166][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:01.167][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:01.169][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:29:01.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:29:01.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:01.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:01.175][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:29:01.177][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:29:01.178][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:01.179][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:01.181][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:29:01.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:29:01.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:01.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:01.187][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:29:01.189][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:29:01.190][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:01.191][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:01.193][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:29:01.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:29:01.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:01.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:01.199][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:29:01.200][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:29:01.202][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:01.203][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:01.205][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:29:01.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:29:01.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:01.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:01.210][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:01.212][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:01.213][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:01.215][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:01.216][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:29:01.218][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:01.219][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:01.221][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:01.222][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:29:01.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:01.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:01.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:01.228][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:01.230][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:01.231][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:01.232][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:01.234][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:01.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:01.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:01.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:01.240][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:29:01.241][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:29:01.243][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:01.244][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:01.246][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:29:01.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:29:01.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:01.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:01.252][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:29:01.253][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:29:01.254][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:01.256][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:01.258][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:29:01.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:29:01.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:01.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:01.263][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:29:01.265][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:29:01.266][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:01.267][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:01.269][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:29:01.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:29:01.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:01.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:01.275][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:01.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:01.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:01.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:01.281][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:01.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:01.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:01.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:01.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:01.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:01.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:01.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:01.292][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:01.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:01.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:01.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:01.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:01.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:01.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:01.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:01.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:01.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:01.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:01.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:01.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:01.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:01.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:01.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:01.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:01.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:01.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:01.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:01.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:01.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:01.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:01.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:01.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:01.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:01.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:01.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:01.331][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2025-04-17 04:29:01.333][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:01.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:01.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:01.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:01.338][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:01.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:01.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:01.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:01.344][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:01.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:01.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:01.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:01.349][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:01.350][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:01.352][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:01.370][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:01.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:01.372][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:01.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:01.375][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2025-04-17 04:29:01.377][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-17 04:29:01.379][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2025-04-17 04:29:01.381][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-17 04:29:01.382][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-17 04:29:01.383][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-17 04:29:01.385][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-17 04:29:01.386][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-17 04:29:01.388][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-17 04:29:01.391][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:01.392][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:01.394][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:01.400][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:01.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:01.403][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:01.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:01.406][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2025-04-17 04:29:01.410][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:29:01.411][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:29:01.413][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2025-04-17 04:29:02.211][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2025-04-17 04:29:03.013][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:29:03.016][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2025-04-17 04:29:03.021][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2025-04-17 04:29:03.024][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2025-04-17 04:29:03.026][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-17 04:29:03.028][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-17 04:29:03.030][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-17 04:29:03.032][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:03.034][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:03.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:03.041][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:03.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:03.044][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:03.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:03.049][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:03.050][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:03.051][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:03.053][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:03.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:03.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:03.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:03.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:03.060][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:29:03.062][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:29:03.063][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:03.064][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:03.066][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:29:03.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:29:03.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:03.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:03.072][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:29:03.073][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:29:03.074][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:03.076][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:03.077][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:29:03.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:29:03.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:03.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:03.083][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:29:03.085][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:29:03.086][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:03.088][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:03.089][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:29:03.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:29:03.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:03.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:03.095][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:29:03.097][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:29:03.098][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:03.099][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:03.101][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:29:03.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:29:03.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:03.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:03.107][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:03.109][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:03.110][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:03.112][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:03.113][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:29:03.115][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:03.116][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:03.118][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:03.120][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:29:03.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:03.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:03.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:03.126][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:03.127][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:03.129][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:03.130][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:03.132][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:03.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:03.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:03.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:03.137][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:29:03.139][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:29:03.140][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:03.142][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:03.144][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:29:03.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:29:03.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:03.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:03.149][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:29:03.151][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:29:03.152][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:03.154][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:03.155][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:29:03.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:29:03.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:03.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:03.161][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:29:03.162][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:29:03.164][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:03.165][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:03.167][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:29:03.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:29:03.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:03.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:03.173][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:03.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:03.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:03.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:03.178][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:03.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:03.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:03.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:03.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:03.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:03.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:03.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:03.190][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:03.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:03.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:03.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:03.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:03.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:03.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:03.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:03.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:03.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:03.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:03.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:03.207][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:03.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:03.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:03.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:03.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:03.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:03.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:03.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:03.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:03.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:03.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:03.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:03.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:03.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:03.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:03.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:03.241][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2025-04-17 04:29:03.243][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:03.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:03.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:03.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:03.249][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:03.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:03.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:03.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:03.254][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:03.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:03.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:03.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:03.260][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:03.261][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:03.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:03.269][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:03.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:03.272][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:03.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:03.274][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2025-04-17 04:29:03.276][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-17 04:29:03.278][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2025-04-17 04:29:03.280][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-17 04:29:03.282][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-17 04:29:03.283][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-17 04:29:03.285][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-17 04:29:03.286][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-17 04:29:03.288][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-17 04:29:03.292][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:03.293][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:03.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:03.301][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:03.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:03.304][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:03.305][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[2025-04-17 04:29:03.306][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2025-04-17 04:29:03.310][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:29:03.312][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:29:03.320][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2025-04-17 04:29:04.067][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2025-04-17 04:29:04.787][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:29:04.791][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2025-04-17 04:29:04.796][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2025-04-17 04:29:04.800][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2025-04-17 04:29:04.802][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-17 04:29:04.804][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-17 04:29:04.806][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-17 04:29:04.809][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:04.810][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:04.812][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:04.820][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:04.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:04.823][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:04.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:04.828][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:04.830][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:04.831][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:04.833][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:04.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:04.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:04.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:04.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:04.841][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:29:04.842][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:29:04.844][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:04.845][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:04.847][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:29:04.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:29:04.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:04.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:04.853][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:29:04.855][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:29:04.856][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:04.858][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:04.860][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:29:04.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:29:04.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:04.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:04.866][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:29:04.868][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:29:04.869][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:04.871][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:04.873][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:29:04.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:29:04.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:04.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:04.879][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:29:04.881][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:29:04.882][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:04.884][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:04.886][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:29:04.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:29:04.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:04.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:04.892][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:04.894][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:04.895][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:04.897][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:04.898][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:29:04.900][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:04.902][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:04.903][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:04.905][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:29:04.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:04.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:04.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:04.911][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:04.912][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:04.914][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:04.915][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:04.917][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:04.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:04.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:04.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:04.923][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:29:04.925][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:29:04.926][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:04.928][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:04.930][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:29:04.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:29:04.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:04.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:04.936][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:29:04.938][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:29:04.939][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:04.940][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:04.942][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:29:04.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:29:04.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:04.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:04.948][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:29:04.950][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:29:04.951][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:04.953][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:04.955][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:29:04.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:29:04.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:04.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:04.961][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:04.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:04.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:05.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:05.038][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:05.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:05.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:05.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:05.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:05.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:05.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:05.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:05.049][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:05.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:05.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:05.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:05.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:05.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:05.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:05.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:05.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:05.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:05.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:05.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:05.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:05.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:05.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:05.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:05.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:05.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:05.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:05.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:05.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:05.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:05.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:05.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:05.084][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:05.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:05.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:05.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:05.090][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2025-04-17 04:29:05.092][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:05.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:05.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:05.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:05.098][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:05.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:05.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:05.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:05.103][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:05.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:05.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:05.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:05.109][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:05.110][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:05.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:05.118][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:05.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:05.121][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:05.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:05.124][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2025-04-17 04:29:05.126][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-17 04:29:05.128][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2025-04-17 04:29:05.129][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-17 04:29:05.131][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-17 04:29:05.133][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-17 04:29:05.134][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-17 04:29:05.136][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-17 04:29:05.137][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-17 04:29:05.141][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:05.142][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:05.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:05.150][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:05.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:05.152][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:05.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:05.155][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2025-04-17 04:29:05.159][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:29:05.161][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:29:05.163][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2025-04-17 04:29:05.904][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2025-04-17 04:29:06.652][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:29:06.655][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2025-04-17 04:29:06.659][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2025-04-17 04:29:06.663][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2025-04-17 04:29:06.665][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-17 04:29:06.667][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-17 04:29:06.668][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-17 04:29:06.671][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:06.672][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:06.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:06.680][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:06.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:06.683][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:06.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:06.687][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:06.689][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:06.690][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:06.691][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:06.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:06.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:06.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:06.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:06.699][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:29:06.700][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:29:06.702][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:06.703][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:06.705][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:29:06.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:29:06.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:06.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:06.711][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:29:06.712][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:29:06.713][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:06.715][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:06.717][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:29:06.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:29:06.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:06.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:06.723][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:29:06.724][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:29:06.726][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:06.727][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:06.729][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:29:06.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:29:06.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:06.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:06.734][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:29:06.736][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:29:06.737][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:06.738][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:06.740][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:29:06.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:29:06.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:06.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:06.745][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:06.747][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:06.748][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:06.749][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:06.751][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:29:06.753][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:06.754][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:06.756][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:06.758][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:29:06.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:06.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:06.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:06.764][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:06.765][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:06.766][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:06.768][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:06.769][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:06.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:06.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:06.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:06.775][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:29:06.776][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:29:06.778][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:06.779][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:06.781][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:29:06.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:29:06.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:06.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:06.799][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:29:06.800][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:29:06.802][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:06.803][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:06.805][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:29:06.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:29:06.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:06.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:06.810][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:29:06.812][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:29:06.813][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:06.814][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:06.816][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:29:06.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:29:06.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:06.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:06.821][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:06.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:06.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:06.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:06.827][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:06.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:06.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:06.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:06.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:06.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:06.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:06.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:06.838][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:06.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:06.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:06.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:06.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:06.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:06.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:06.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:06.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:06.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:06.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:06.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:06.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:06.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:06.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:06.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:06.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:06.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:06.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:06.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:06.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:06.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:06.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:06.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:06.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:06.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:06.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:06.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:06.880][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2025-04-17 04:29:06.881][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:06.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:06.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:06.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:06.887][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:06.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:06.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:06.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:06.893][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:06.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:06.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:06.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:06.899][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:06.901][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:06.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:06.909][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:06.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:06.911][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:06.913][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[2025-04-17 04:29:06.914][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2025-04-17 04:29:06.916][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-17 04:29:06.918][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2025-04-17 04:29:06.920][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-17 04:29:06.922][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-17 04:29:06.924][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-17 04:29:06.925][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-17 04:29:06.927][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-17 04:29:06.928][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-17 04:29:06.932][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:06.933][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:06.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:06.941][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:06.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:06.944][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:06.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:06.947][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2025-04-17 04:29:06.951][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:29:06.953][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:29:06.955][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2025-04-17 04:29:07.732][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2025-04-17 04:29:08.485][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:29:08.488][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2025-04-17 04:29:08.492][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2025-04-17 04:29:08.495][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2025-04-17 04:29:08.497][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-17 04:29:08.499][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-17 04:29:08.500][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-17 04:29:08.503][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:08.504][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:08.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:08.511][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:08.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:08.514][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:08.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:08.518][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:08.520][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:08.521][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:08.522][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:08.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:08.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:08.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:08.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:08.530][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:29:08.531][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:29:08.533][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:08.534][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:08.536][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:29:08.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:29:08.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:08.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:08.542][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:29:08.543][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:29:08.544][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:08.546][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:08.547][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:29:08.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:29:08.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:08.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:08.553][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:29:08.555][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:29:08.556][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:08.557][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:08.559][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:29:08.561][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:29:08.562][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:08.563][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:08.565][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:08.566][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:08.568][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:08.569][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:08.571][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:29:08.572][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:08.573][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:08.575][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:08.576][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:29:08.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:08.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:08.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:08.594][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:08.596][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:08.597][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:08.598][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:08.600][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:08.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:08.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:08.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:08.606][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:29:08.607][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:29:08.609][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:08.610][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:08.612][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:29:08.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:29:08.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:08.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:08.618][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:29:08.619][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:29:08.621][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:08.622][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:08.624][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:29:08.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:29:08.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:08.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:08.629][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:29:08.631][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:29:08.632][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:08.633][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:08.635][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:08.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:08.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:08.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:08.641][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:08.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:08.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:08.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:08.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:08.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:08.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:08.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:08.652][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:08.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:08.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:08.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:08.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:08.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:08.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:08.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:08.663][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:08.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:08.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:08.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:08.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:08.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:08.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:08.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:08.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:08.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:08.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:08.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:08.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:08.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:08.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:08.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:08.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:08.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:08.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:08.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:08.691][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2025-04-17 04:29:08.692][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:08.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:08.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:08.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:08.698][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:08.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:08.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:08.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:08.703][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:08.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:08.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:08.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:08.709][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:08.710][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:08.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:08.718][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:08.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:08.720][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:08.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:08.723][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2025-04-17 04:29:08.725][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-17 04:29:08.727][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2025-04-17 04:29:08.728][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-17 04:29:08.730][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-17 04:29:08.731][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-17 04:29:08.733][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-17 04:29:08.734][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-17 04:29:08.735][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-17 04:29:08.739][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:08.740][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:08.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:08.748][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:08.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:08.751][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:08.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:08.754][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2025-04-17 04:29:08.757][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:29:08.759][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:29:08.761][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2025-04-17 04:29:09.502][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2025-04-17 04:29:10.256][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:29:10.258][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2025-04-17 04:29:10.263][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2025-04-17 04:29:10.267][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2025-04-17 04:29:10.275][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-17 04:29:10.278][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-17 04:29:10.280][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-17 04:29:10.283][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:10.285][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:10.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:10.295][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:10.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:10.298][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:10.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:10.304][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:10.305][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:10.307][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:10.308][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:10.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:10.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:10.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:10.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:10.317][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:29:10.318][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:29:10.320][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:10.321][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:10.323][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:29:10.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:29:10.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:10.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:10.330][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:29:10.331][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:29:10.333][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:10.334][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:10.336][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:29:10.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:29:10.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:10.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:10.343][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:29:10.344][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:29:10.346][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:10.347][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:10.349][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:29:10.351][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:29:10.352][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:10.369][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:10.378][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:10.379][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:10.381][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:10.382][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:10.384][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:29:10.386][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:10.388][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:10.389][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:10.391][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:29:10.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:10.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:10.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:10.398][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:10.400][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:10.401][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:10.403][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:10.405][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:10.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:10.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:10.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:10.412][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:29:10.413][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:29:10.415][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:10.416][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:10.419][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:29:10.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:29:10.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:10.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:10.425][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:29:10.427][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:29:10.428][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:10.430][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:10.431][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:29:10.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:29:10.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:10.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:10.438][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:29:10.439][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:29:10.441][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:10.442][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:10.444][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:10.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:10.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:10.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:10.451][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:10.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:10.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:10.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:10.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:10.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:10.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:10.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:10.464][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:10.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:10.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:10.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:10.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:10.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:10.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:10.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:10.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:10.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:10.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:10.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:10.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:10.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:10.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:10.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:10.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:10.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:10.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:10.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:10.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:10.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:10.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:10.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:10.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:10.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:10.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:10.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:10.506][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2025-04-17 04:29:10.508][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:10.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:10.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:10.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:10.514][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:10.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:10.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:10.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:10.520][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:10.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:10.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:10.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:10.526][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:10.527][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:10.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:10.535][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:10.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:10.538][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:10.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:10.541][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2025-04-17 04:29:10.543][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-17 04:29:10.546][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2025-04-17 04:29:10.548][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-17 04:29:10.549][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-17 04:29:10.551][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-17 04:29:10.553][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-17 04:29:10.554][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-17 04:29:10.556][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-17 04:29:10.560][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:10.561][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:10.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:10.569][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:10.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:10.572][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:10.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:10.575][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2025-04-17 04:29:10.579][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:29:10.581][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:29:10.583][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2025-04-17 04:29:11.312][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2025-04-17 04:29:12.036][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:29:12.039][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2025-04-17 04:29:12.043][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2025-04-17 04:29:12.047][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2025-04-17 04:29:12.049][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-17 04:29:12.050][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-17 04:29:12.052][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-17 04:29:12.054][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:12.055][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:12.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:12.063][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:12.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:12.066][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:12.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:12.070][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:12.072][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:12.073][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:12.074][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:12.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:12.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:12.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:12.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:12.081][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:29:12.083][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:29:12.084][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:12.086][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:12.087][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:29:12.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:29:12.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:12.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:12.093][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:29:12.094][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:29:12.095][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:12.097][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:12.111][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:29:12.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:29:12.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:12.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:12.116][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:29:12.118][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:29:12.119][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:12.120][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:12.122][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:29:12.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:29:12.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:12.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:12.127][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:29:12.129][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:29:12.130][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:12.132][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:12.133][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:29:12.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:29:12.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:12.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:12.139][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:12.140][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:12.141][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:12.143][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:12.145][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:29:12.146][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:12.147][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:12.149][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:12.150][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:29:12.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:12.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:12.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:12.156][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:12.157][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:12.159][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:12.160][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:12.162][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:12.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:12.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:12.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:12.167][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:29:12.169][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:29:12.170][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:12.171][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:12.173][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:29:12.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:29:12.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:12.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:12.179][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:29:12.180][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:29:12.181][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:12.183][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:12.184][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:29:12.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:29:12.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:12.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:12.190][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:29:12.191][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:29:12.193][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:12.194][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:12.196][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:29:12.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:29:12.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:12.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:12.201][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:12.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:12.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:12.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:12.207][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:12.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:12.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:12.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:12.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:12.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:12.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:12.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:12.218][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:12.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:12.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:12.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:12.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:12.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:12.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:12.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:12.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:12.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:12.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:12.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:12.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:12.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:12.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:12.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:12.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:12.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:12.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:12.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:12.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:12.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:12.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:12.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:12.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:12.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:12.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:12.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:12.257][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2025-04-17 04:29:12.258][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:12.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:12.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:12.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:12.263][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:12.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:12.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:12.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:12.269][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:12.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:12.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:12.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:12.274][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:12.276][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:12.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:12.283][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:12.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:12.286][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:12.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:12.289][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2025-04-17 04:29:12.290][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-17 04:29:12.292][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2025-04-17 04:29:12.294][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-17 04:29:12.296][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-17 04:29:12.297][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-17 04:29:12.299][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-17 04:29:12.300][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-17 04:29:12.302][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-17 04:29:12.306][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:12.307][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:12.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:12.315][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:12.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:12.317][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:12.319][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[2025-04-17 04:29:12.320][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2025-04-17 04:29:12.324][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:29:12.326][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:29:12.327][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2025-04-17 04:29:13.161][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2025-04-17 04:29:13.906][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:29:13.909][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2025-04-17 04:29:13.914][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2025-04-17 04:29:13.918][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2025-04-17 04:29:13.919][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-17 04:29:13.921][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-17 04:29:13.923][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-17 04:29:13.925][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:13.926][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:13.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:13.934][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:13.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:13.950][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:13.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:13.955][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:13.956][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:13.958][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:13.959][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:13.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:13.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:13.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:13.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:13.967][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:29:13.968][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:29:13.970][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:13.971][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:13.973][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:29:13.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:29:13.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:13.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:13.979][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:29:13.980][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:29:13.982][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:13.983][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:13.985][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:29:13.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:29:13.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:13.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:13.991][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:29:13.993][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:29:13.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:13.995][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:13.997][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:29:13.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:29:14.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:14.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:14.003][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:29:14.005][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:29:14.006][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:14.007][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:14.009][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:29:14.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:29:14.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:14.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:14.015][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:14.017][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:14.018][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:14.020][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:14.021][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:29:14.023][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:14.024][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:14.026][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:14.027][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:29:14.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:14.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:14.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:14.038][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:14.039][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:14.041][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:14.042][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:14.044][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:14.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:14.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:14.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:14.049][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:29:14.051][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:29:14.052][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:14.053][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:14.055][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:29:14.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:29:14.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:14.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:14.061][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:29:14.063][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:29:14.064][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:14.066][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:14.067][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:29:14.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:29:14.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:14.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:14.073][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:29:14.075][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:29:14.076][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:14.078][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:14.079][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:29:14.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:29:14.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:14.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:14.085][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:14.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:14.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:14.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:14.091][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:14.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:14.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:14.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:14.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:14.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:14.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:14.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:14.103][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:14.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:14.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:14.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:14.109][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:14.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:14.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:14.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:14.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:14.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:14.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:14.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:14.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:14.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:14.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:14.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:14.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:14.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:14.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:14.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:14.132][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:14.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:14.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:14.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:14.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:14.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:14.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:14.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:14.143][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2025-04-17 04:29:14.145][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:14.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:14.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:14.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:14.151][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:14.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:14.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:14.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:14.156][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:14.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:14.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:14.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:14.162][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:14.163][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:14.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:14.171][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:14.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:14.174][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:14.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:14.177][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2025-04-17 04:29:14.179][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-17 04:29:14.181][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2025-04-17 04:29:14.182][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-17 04:29:14.184][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-17 04:29:14.186][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-17 04:29:14.187][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-17 04:29:14.188][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-17 04:29:14.190][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-17 04:29:14.194][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:14.195][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:14.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:14.203][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:14.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:14.206][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:14.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:14.208][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2025-04-17 04:29:14.212][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:29:14.222][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:29:14.224][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2025-04-17 04:29:14.954][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2025-04-17 04:29:15.720][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:29:15.722][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2025-04-17 04:29:15.727][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2025-04-17 04:29:15.730][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2025-04-17 04:29:15.732][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-17 04:29:15.734][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-17 04:29:15.735][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-17 04:29:15.737][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:15.739][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:15.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:15.747][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:15.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:15.749][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:15.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:15.754][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:15.755][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:15.757][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:15.758][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:15.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:15.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:15.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:15.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:15.765][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:29:15.767][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:29:15.768][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:15.769][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:15.771][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:29:15.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:29:15.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:15.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:15.777][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:29:15.778][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:29:15.779][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:15.781][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:15.782][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:29:15.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:29:15.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:15.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:15.788][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:29:15.789][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:29:15.791][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:15.792][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:15.794][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:29:15.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:29:15.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:15.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:15.800][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:29:15.801][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:29:15.802][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:15.804][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:15.805][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:29:15.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:29:15.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:15.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:15.811][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:15.813][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:15.814][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:15.815][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:15.823][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:29:15.826][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:15.827][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:15.828][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:15.830][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:29:15.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:15.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:15.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:15.836][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:15.838][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:15.839][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:15.841][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:15.843][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:15.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:15.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:15.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:15.849][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:29:15.850][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:29:15.852][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:15.853][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:15.855][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:29:15.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:29:15.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:15.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:15.862][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:29:15.863][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:29:15.865][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:15.866][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:15.868][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:29:15.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:29:15.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:15.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:15.874][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:29:15.876][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:29:15.877][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:15.879][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:15.880][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:29:15.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:29:15.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:15.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:15.887][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:15.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:15.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:15.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:15.893][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:15.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:15.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:15.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:15.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:15.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:15.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:15.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:15.905][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:15.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:15.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:15.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:15.911][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:15.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:15.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:15.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:15.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:15.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:15.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:15.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:15.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:15.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:15.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:15.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:15.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:15.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:15.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:15.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:15.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:15.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:15.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:15.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:15.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:15.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:15.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:15.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:15.948][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2025-04-17 04:29:15.950][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:15.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:15.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:15.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:15.956][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:15.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:15.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:15.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:15.962][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:15.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:15.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:15.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:15.968][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:15.970][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:15.971][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:15.979][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:15.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:15.982][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:15.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:16.006][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2025-04-17 04:29:16.008][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-17 04:29:16.011][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2025-04-17 04:29:16.013][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-17 04:29:16.015][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-17 04:29:16.017][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-17 04:29:16.018][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-17 04:29:16.020][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-17 04:29:16.021][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-17 04:29:16.025][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:16.027][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:16.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:16.035][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:16.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:16.038][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:16.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:16.041][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2025-04-17 04:29:16.045][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:29:16.047][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:29:16.049][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2025-04-17 04:29:16.777][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2025-04-17 04:29:17.539][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:29:17.543][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2025-04-17 04:29:17.547][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2025-04-17 04:29:17.551][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2025-04-17 04:29:17.553][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-17 04:29:17.555][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-17 04:29:17.557][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-17 04:29:17.559][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:17.561][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:17.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:17.569][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:17.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:17.571][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:17.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:17.576][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:17.578][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:17.579][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:17.581][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:17.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:17.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:17.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:17.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:17.588][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:29:17.590][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:29:17.591][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:17.593][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:17.595][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:29:17.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:29:17.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:17.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:17.601][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:29:17.602][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:29:17.604][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:17.605][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:17.607][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:29:17.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:29:17.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:17.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:17.613][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:29:17.614][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:29:17.616][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:17.617][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:17.619][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:29:17.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:29:17.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:17.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:17.625][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:29:17.626][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:29:17.628][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:17.629][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:17.631][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:29:17.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:29:17.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:17.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:17.637][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:17.638][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:17.639][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:17.641][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:17.643][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:29:17.644][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:17.645][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:17.647][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:17.648][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:29:17.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:17.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:17.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:17.654][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:17.656][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:17.657][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:17.659][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:17.660][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:17.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:17.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:17.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:17.666][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:29:17.668][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:29:17.669][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:17.671][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:17.673][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:29:17.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:29:17.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:17.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:17.678][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:29:17.680][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:29:17.681][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:17.683][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:17.684][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:29:17.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:29:17.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:17.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:17.690][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:29:17.692][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:29:17.693][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:17.694][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:17.696][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:29:17.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:29:17.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:17.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:17.702][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:17.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:17.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:17.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:17.708][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:17.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:17.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:17.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:17.714][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:17.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:17.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:17.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:17.719][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:17.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:17.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:17.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:17.725][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:17.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:17.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:17.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:17.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:17.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:17.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:17.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:17.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:17.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:17.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:17.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:17.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:17.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:17.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:17.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:17.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:17.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:17.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:17.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:17.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:17.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:17.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:17.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:17.772][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2025-04-17 04:29:17.774][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:17.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:17.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:17.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:17.780][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:17.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:17.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:17.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:17.786][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:17.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:17.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:17.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:17.791][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:17.793][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:17.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:17.800][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:17.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:17.803][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:17.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:17.806][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2025-04-17 04:29:17.808][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-17 04:29:17.810][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2025-04-17 04:29:17.812][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-17 04:29:17.813][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-17 04:29:17.815][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-17 04:29:17.816][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-17 04:29:17.818][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-17 04:29:17.819][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-17 04:29:17.823][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:17.824][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:17.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:17.833][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:17.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:17.836][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:17.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:17.839][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2025-04-17 04:29:17.843][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:29:17.844][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:29:17.847][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2025-04-17 04:29:18.597][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2025-04-17 04:29:19.396][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:29:19.399][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2025-04-17 04:29:19.403][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2025-04-17 04:29:19.407][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2025-04-17 04:29:19.409][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-17 04:29:19.411][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-17 04:29:19.412][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-17 04:29:19.414][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:19.416][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:19.417][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:19.423][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:19.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:19.426][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:19.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:19.430][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:19.432][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:19.433][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:19.434][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:19.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:19.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:19.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:19.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:19.442][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:29:19.443][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:29:19.444][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:19.446][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:19.447][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:29:19.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:29:19.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:19.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:19.453][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:29:19.454][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:29:19.456][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:19.457][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:19.459][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:29:19.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:29:19.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:19.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:19.464][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:29:19.466][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:29:19.467][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:19.469][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:19.470][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:29:19.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:29:19.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:19.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:19.476][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:29:19.477][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:29:19.479][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:19.480][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:19.482][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:29:19.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:29:19.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:19.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:19.487][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:19.489][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:19.490][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:19.491][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:19.493][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:29:19.495][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:19.496][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:19.497][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:19.499][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:29:19.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:19.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:19.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:19.505][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:19.506][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:19.507][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:19.509][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:19.510][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:19.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:19.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:19.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:19.516][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:29:19.518][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:29:19.519][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:19.520][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:19.522][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:29:19.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:29:19.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:19.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:19.528][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:29:19.529][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:29:19.530][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:19.532][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:19.533][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:29:19.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:29:19.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:19.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:19.539][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:29:19.541][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:29:19.542][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:19.543][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:19.545][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:29:19.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:29:19.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:19.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:19.551][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:19.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:19.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:19.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:19.556][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:19.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:19.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:19.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:19.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:19.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:19.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:19.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:19.567][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:19.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:19.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:19.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:19.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:19.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:19.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:19.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:19.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:19.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:19.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:19.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:19.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:19.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:19.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:19.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:19.601][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:19.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:19.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:19.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:19.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:19.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:19.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:19.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:19.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:19.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:19.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:19.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:19.618][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2025-04-17 04:29:19.619][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:19.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:19.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:19.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:19.624][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:19.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:19.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:19.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:19.630][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:19.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:19.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:19.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:19.635][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:19.636][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:19.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:19.644][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:19.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:19.646][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:19.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:19.649][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2025-04-17 04:29:19.650][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-17 04:29:19.653][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2025-04-17 04:29:19.654][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-17 04:29:19.656][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-17 04:29:19.657][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-17 04:29:19.659][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-17 04:29:19.660][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-17 04:29:19.661][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-17 04:29:19.665][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:19.666][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:19.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:19.674][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:19.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:19.677][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:19.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:19.680][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2025-04-17 04:29:19.684][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:29:19.685][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:29:19.687][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2025-04-17 04:29:20.431][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2025-04-17 04:29:21.166][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:29:21.170][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2025-04-17 04:29:21.174][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2025-04-17 04:29:21.178][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2025-04-17 04:29:21.181][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-17 04:29:21.182][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-17 04:29:21.184][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-17 04:29:21.187][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:21.188][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:21.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:21.196][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:21.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:21.199][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:21.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:21.204][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:21.205][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:21.207][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:21.208][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:21.210][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:21.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:21.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:21.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:21.216][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:29:21.218][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:29:21.219][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:21.221][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:21.223][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:29:21.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:29:21.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:21.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:21.229][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:29:21.231][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:29:21.232][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:21.234][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:21.236][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:29:21.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:29:21.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:21.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:21.242][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:29:21.244][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:29:21.245][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:21.246][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:21.248][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:29:21.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:29:21.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:21.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:21.254][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:29:21.256][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:29:21.257][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:21.258][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:21.260][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:29:21.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:29:21.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:21.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:21.266][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:21.267][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:21.269][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:21.270][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:21.272][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:29:21.273][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:21.275][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:21.276][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:21.278][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:29:21.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:21.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:21.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:21.284][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:21.285][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:21.287][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:21.288][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:21.290][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:21.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:21.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:21.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:21.296][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:29:21.298][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:29:21.299][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:21.301][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:21.303][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:29:21.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:29:21.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:21.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:21.308][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:29:21.310][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:29:21.311][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:21.313][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:21.322][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:29:21.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:29:21.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:21.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:21.333][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:29:21.335][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:29:21.336][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:21.337][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:21.339][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:29:21.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:29:21.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:21.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:21.345][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:21.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:21.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:21.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:21.350][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:21.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:21.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:21.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:21.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:21.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:21.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:21.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:21.370][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:21.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:21.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:21.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:21.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:21.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:21.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:21.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:21.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:21.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:21.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:21.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:21.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:21.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:21.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:21.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:21.395][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:21.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:21.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:21.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:21.401][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:21.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:21.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:21.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:21.407][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:21.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:21.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:21.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:21.413][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2025-04-17 04:29:21.415][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:21.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:21.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:21.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:21.421][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:21.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:21.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:21.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:21.427][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:21.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:21.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:21.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:21.434][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:21.435][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:21.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:21.445][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:21.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:21.447][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:21.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:21.450][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2025-04-17 04:29:21.452][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-17 04:29:21.455][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2025-04-17 04:29:21.456][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-17 04:29:21.458][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-17 04:29:21.460][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-17 04:29:21.461][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-17 04:29:21.463][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-17 04:29:21.464][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-17 04:29:21.468][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:21.470][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:21.471][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:21.478][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:21.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:21.481][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:21.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:21.484][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2025-04-17 04:29:21.488][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:29:21.489][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:29:21.492][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2025-04-17 04:29:22.237][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2025-04-17 04:29:23.000][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:29:23.004][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2025-04-17 04:29:23.012][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2025-04-17 04:29:23.017][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2025-04-17 04:29:23.019][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-17 04:29:23.022][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-17 04:29:23.024][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-17 04:29:23.028][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:23.030][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:23.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:23.041][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:23.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:23.044][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:23.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:23.053][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:23.056][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:23.058][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:23.060][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:23.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:23.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:23.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:23.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:23.071][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:29:23.073][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:29:23.075][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:23.077][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:23.080][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:29:23.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:29:23.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:23.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:23.087][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:29:23.089][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:29:23.091][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:23.093][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:23.096][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:29:23.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:29:23.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:23.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:23.103][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:29:23.105][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:29:23.107][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:23.109][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:23.111][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:29:23.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:29:23.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:23.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:23.119][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:29:23.121][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:29:23.123][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:23.125][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:23.127][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:29:23.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:29:23.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:23.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:23.134][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:23.136][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:23.138][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:23.140][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:23.142][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:29:23.144][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:23.146][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:23.189][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:23.194][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:29:23.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:23.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:23.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:23.203][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:23.205][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:23.207][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:23.209][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:23.211][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:23.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:23.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:23.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:23.219][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:29:23.222][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:29:23.223][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:23.225][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:23.228][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:29:23.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:29:23.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:23.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:23.234][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:29:23.235][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:29:23.237][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:23.238][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:23.240][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:29:23.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:29:23.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:23.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:23.246][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:29:23.247][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:29:23.249][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:23.250][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:23.252][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:29:23.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:29:23.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:23.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:23.258][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:23.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:23.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:23.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:23.263][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:23.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:23.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:23.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:23.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:23.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:23.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:23.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:23.274][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:23.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:23.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:23.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:23.279][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:23.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:23.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:23.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:23.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:23.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:23.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:23.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:23.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:23.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:23.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:23.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:23.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:23.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:23.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:23.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:23.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:23.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:23.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:23.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:23.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:23.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:23.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:23.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:23.313][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2025-04-17 04:29:23.314][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:23.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:23.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:23.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:23.320][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:23.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:23.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:23.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:23.325][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:23.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:23.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:23.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:23.356][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[2025-04-17 04:29:23.361][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:29:23.362][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:29:23.365][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-17 04:29:24.196][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-17 04:29:25.116][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:29:25.119][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-04-17 04:29:25.125][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-04-17 04:29:25.129][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:25.130][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:25.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:25.139][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:25.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:25.141][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:25.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:25.144][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.150][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.155][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:25.160][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:25.162][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:25.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:25.169][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:25.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:25.172][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:25.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:25.175][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.180][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.186][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.191][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.196][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:25.215][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:25.217][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:25.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:25.224][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:25.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:25.227][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:25.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:25.230][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.235][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.241][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.246][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.252][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:25.257][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:25.259][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:25.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:25.266][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:25.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:25.269][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:25.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:25.271][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.277][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.282][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.288][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.293][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:25.299][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:25.300][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:25.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:25.307][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:25.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:25.310][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:25.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:25.313][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.318][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.323][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:25.329][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:25.330][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:25.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:25.337][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:25.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:25.340][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:25.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:25.343][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.348][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.354][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:25.359][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:25.361][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:25.362][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:25.368][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:25.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:25.371][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:25.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:25.374][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.380][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.385][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:25.391][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:25.392][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:25.394][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:25.400][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:25.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:25.403][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:25.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:25.406][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.412][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.418][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:25.423][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:25.425][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:25.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:25.432][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:25.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:25.435][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:25.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:25.438][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.443][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.449][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:25.454][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:25.456][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:25.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:25.472][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:25.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:25.475][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:25.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:25.477][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.483][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.489][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:25.495][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:25.496][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:25.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:25.504][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:25.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:25.507][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:25.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:25.510][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.515][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.521][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:25.527][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:25.528][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:25.529][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:25.536][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:25.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:25.539][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:25.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:25.542][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.547][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.553][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:25.559][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:25.560][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:25.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:25.568][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:25.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:25.570][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:25.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:25.573][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.579][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.585][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:25.590][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:25.592][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:25.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:25.600][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:25.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:25.602][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:25.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:25.605][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.611][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.616][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:25.622][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:25.623][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:25.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:25.631][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:25.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:25.634][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:25.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:25.637][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.643][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.649][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:25.655][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:25.656][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:25.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:25.664][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:25.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:25.675][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:25.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:25.680][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.688][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.697][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:25.706][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:25.708][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:25.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:25.721][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:25.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:25.725][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:25.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:25.730][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.738][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.747][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:25.755][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:25.757][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:25.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:25.791][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:25.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:25.797][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:25.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:25.801][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.810][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.818][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:25.826][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:25.829][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:25.830][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:25.837][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:25.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:25.840][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:25.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:25.843][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.850][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.856][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:25.862][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:25.864][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:25.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:25.872][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:25.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:25.875][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:25.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:25.878][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.885][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.891][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:25.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.919][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:25.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:25.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.926][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:25.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:25.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.932][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:25.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:25.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.939][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:25.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:25.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:25.945][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:25.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:25.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:25.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:25.999][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-17 04:29:26.005][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:29:26.007][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:29:26.010][private$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[2025-04-17 04:29:26.822][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[2025-04-17 04:29:27.554][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:29:27.557][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2025-04-17 04:29:27.562][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2025-04-17 04:29:27.567][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[2025-04-17 04:29:27.571][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:29:27.573][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:29:27.575][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-17 04:29:28.302][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-17 04:29:29.142][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:29:29.145][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2025-04-17 04:29:29.150][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2025-04-17 04:29:29.154][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:29.156][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:29.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:29.163][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:29.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:29.166][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:29.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:29.169][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2025-04-17 04:29:29.170][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-17 04:29:29.172][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2025-04-17 04:29:29.174][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-17 04:29:29.175][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-17 04:29:29.194][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-17 04:29:29.196][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-17 04:29:29.197][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-17 04:29:29.198][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-17 04:29:29.202][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:29.204][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:29.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:29.211][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:29.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:29.214][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:29.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:29.217][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2025-04-17 04:29:29.220][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:29:29.222][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:29:29.224][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2025-04-17 04:29:29.956][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2025-04-17 04:29:32.254][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:29:32.257][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2025-04-17 04:29:32.261][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2025-04-17 04:29:32.265][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2025-04-17 04:29:32.267][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-17 04:29:32.269][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-17 04:29:32.270][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-17 04:29:32.273][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:32.274][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:32.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:32.282][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:32.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:32.285][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:32.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:32.290][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:32.291][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:32.293][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:32.294][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:32.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:32.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:32.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:32.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:32.302][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:29:32.304][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:29:32.305][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:32.307][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:32.308][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:29:32.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:29:32.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:32.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:32.314][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:29:32.316][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:29:32.317][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:32.318][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:32.321][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:29:32.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:29:32.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:32.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:32.326][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:29:32.328][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:29:32.329][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:32.330][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:32.332][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:29:32.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:29:32.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:32.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:32.338][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:29:32.340][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:29:32.341][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:32.342][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:32.344][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:29:32.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:29:32.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:32.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:32.350][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:32.352][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:32.353][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:32.355][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:32.356][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:32.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:32.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:32.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:32.362][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:29:32.364][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:32.365][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:32.366][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:32.368][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:29:32.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:32.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:32.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:32.375][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:32.377][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:32.378][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:32.379][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:32.381][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:32.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:32.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:32.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:32.387][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:29:32.388][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:29:32.390][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:32.391][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:32.393][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:29:32.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:29:32.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:32.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:32.399][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:29:32.401][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:29:32.402][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:32.403][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:32.405][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:29:32.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:29:32.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:32.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:32.411][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:29:32.413][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:29:32.414][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:32.416][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:32.418][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:29:32.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:29:32.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:32.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:32.424][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:32.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:32.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:32.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:32.430][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:32.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:32.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:32.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:32.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:32.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:32.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:32.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:32.441][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:32.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:32.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:32.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:32.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:32.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:32.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:32.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:32.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:32.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:32.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:32.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:32.459][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:32.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:32.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:32.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:32.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:32.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:32.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:32.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:32.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:32.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:32.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:32.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:32.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:32.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:32.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:32.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:32.495][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2025-04-17 04:29:32.497][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:32.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:32.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:32.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:32.503][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:32.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:32.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:32.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:32.508][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:32.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:32.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:32.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:32.514][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:32.515][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:32.517][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:32.523][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:32.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:32.526][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:32.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:32.529][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:32.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:32.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:32.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:32.535][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:32.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:32.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:32.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:32.540][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:32.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:32.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:32.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:32.546][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:32.547][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:32.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:32.555][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:32.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:32.558][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:32.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:32.561][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2025-04-17 04:29:32.562][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-17 04:29:32.565][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2025-04-17 04:29:32.566][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-17 04:29:32.568][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-17 04:29:32.570][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-17 04:29:32.571][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-17 04:29:32.573][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-17 04:29:32.575][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-17 04:29:32.579][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:32.580][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:32.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:32.589][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:32.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:32.592][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:32.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:32.595][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2025-04-17 04:29:32.599][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:29:32.601][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:29:32.603][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2025-04-17 04:29:33.344][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2025-04-17 04:29:34.176][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:29:34.179][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2025-04-17 04:29:34.183][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2025-04-17 04:29:34.187][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2025-04-17 04:29:34.189][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-17 04:29:34.191][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-17 04:29:34.192][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-17 04:29:34.195][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:34.196][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:34.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:34.204][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:34.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:34.207][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:34.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:34.211][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:34.213][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:34.214][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.215][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:34.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:34.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.222][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:29:34.224][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:29:34.225][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.227][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.228][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:29:34.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:29:34.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.234][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:29:34.236][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:29:34.238][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.239][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.241][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:29:34.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:29:34.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.247][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:29:34.249][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:29:34.250][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.251][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.253][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:29:34.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:29:34.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.259][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:29:34.260][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:29:34.262][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.263][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.265][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:29:34.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:29:34.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.271][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:34.272][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:34.274][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.275][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.277][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:29:34.278][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:34.279][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.281][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.282][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:29:34.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:34.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.288][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.290][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.291][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.293][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.294][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.300][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:29:34.302][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:29:34.303][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.304][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.306][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:29:34.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:29:34.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.312][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:29:34.313][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:29:34.315][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.316][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.318][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:29:34.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:29:34.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.338][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:29:34.340][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:29:34.341][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.343][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.344][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:29:34.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:29:34.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.351][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:34.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:34.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.374][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:34.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:34.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:34.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:34.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.398][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:34.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:34.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:34.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:34.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:34.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:34.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:34.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:34.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:34.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:34.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:34.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:34.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:34.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:34.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:34.465][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2025-04-17 04:29:34.467][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.476][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.485][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:34.540][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-17 04:29:34.548][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-17 04:29:34.551][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-17 04:29:34.554][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-17 04:29:34.557][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-04-17 04:29:34.566][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:34.567][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:34.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:34.579][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:34.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:34.583][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:34.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:34.587][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.596][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.605][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:34.614][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:34.615][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:34.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:34.627][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:34.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:34.631][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:34.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:34.636][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.645][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.655][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.663][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.672][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:34.681][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:34.682][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:34.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:34.693][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:34.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:34.697][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:34.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:34.701][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.711][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.719][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.728][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.736][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:34.745][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:34.746][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:34.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:34.778][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:34.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:34.781][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:34.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:34.786][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.794][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.802][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.808][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.814][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:34.820][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:34.822][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:34.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:34.830][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:34.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:34.832][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:34.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:34.835][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.841][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.848][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:34.854][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:34.855][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:34.856][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:34.863][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:34.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:34.866][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:34.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:34.870][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.876][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.882][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:34.888][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:34.890][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:34.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:34.898][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:34.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:34.901][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:34.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:34.904][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.911][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.917][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:34.924][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:34.925][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:34.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:34.933][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:34.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:34.936][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:34.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:34.940][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.946][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.952][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:34.958][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:34.960][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:34.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:34.968][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:34.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:34.971][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:34.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:34.975][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.982][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:34.988][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:34.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:34.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:34.995][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:34.996][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:34.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:35.006][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:35.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:35.009][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:35.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:35.013][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.020][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.027][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:35.033][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:35.035][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:35.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:35.043][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:35.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:35.046][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:35.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:35.049][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.056][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.072][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:35.078][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:35.079][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:35.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:35.088][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:35.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:35.091][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:35.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:35.094][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.101][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.107][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:35.113][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:35.115][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:35.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:35.123][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:35.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:35.126][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:35.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:35.129][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.135][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.140][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:35.146][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:35.148][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:35.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:35.156][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:35.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:35.159][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:35.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:35.162][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.168][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.174][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:35.179][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:35.180][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:35.182][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:35.188][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:35.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:35.191][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:35.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:35.194][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.200][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.206][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:35.211][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:35.213][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:35.214][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:35.221][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:35.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:35.224][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:35.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:35.227][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.233][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.239][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:35.245][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:35.246][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:35.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:35.255][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:35.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:35.257][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:35.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:35.260][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.266][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.271][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:35.277][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:35.278][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:35.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:35.286][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:35.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:35.289][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:35.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:35.292][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.298][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.303][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:35.309][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:35.310][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:35.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:35.318][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:35.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:35.321][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:35.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:35.324][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.330][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.345][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:35.351][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:35.352][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:35.353][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:35.360][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:35.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:35.363][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:35.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:35.366][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.371][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.377][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:35.408][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-17 04:29:35.413][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-17 04:29:35.415][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-17 04:29:35.417][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-17 04:29:35.419][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-04-17 04:29:35.423][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:35.424][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:35.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:35.433][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:35.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:35.435][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:35.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:35.438][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.444][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.449][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:35.455][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:35.456][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:35.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:35.464][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:35.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:35.466][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:35.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:35.469][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.474][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.480][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.486][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.492][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:35.498][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:35.499][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:35.500][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:35.507][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:35.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:35.510][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:35.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:35.513][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.518][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.523][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.529][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.535][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:35.540][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:35.542][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:35.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:35.549][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:35.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:35.552][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:35.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:35.555][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.560][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.566][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.572][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.577][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:35.583][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:35.584][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:35.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:35.592][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:35.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:35.595][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:35.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:35.612][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.618][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.623][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:35.629][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:35.630][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:35.632][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:35.639][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:35.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:35.641][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:35.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:35.644][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.650][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.655][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:35.661][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:35.662][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:35.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:35.670][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:35.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:35.672][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:35.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:35.675][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.681][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.686][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:35.691][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:35.693][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:35.694][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:35.700][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:35.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:35.703][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:35.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:35.706][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.711][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.716][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:35.722][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:35.723][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:35.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:35.731][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:35.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:35.733][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:35.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:35.736][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.741][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.747][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:35.752][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:35.753][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:35.754][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:35.761][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:35.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:35.763][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:35.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:35.766][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.772][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:35.782][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:35.784][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:35.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:35.808][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:35.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:35.815][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:35.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:35.822][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.831][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.840][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:35.849][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:35.850][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:35.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:35.863][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:35.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:35.867][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:35.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:35.871][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.879][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.887][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:35.894][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:35.896][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:35.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:35.907][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:35.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:35.910][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:35.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:35.968][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.983][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:35.993][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:35.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:35.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:36.000][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:36.002][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:36.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:36.014][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:36.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:36.017][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:36.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:36.022][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:36.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:36.030][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:36.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:36.038][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:36.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:36.045][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:36.047][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:36.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:36.057][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:36.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:36.060][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:36.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:36.064][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:36.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:36.071][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:36.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:36.078][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:36.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:36.085][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:36.087][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:36.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:36.096][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:36.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:36.100][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:36.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:36.103][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:36.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:36.110][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:36.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:36.117][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:36.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:36.124][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:36.126][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:36.127][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:36.136][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:36.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:36.139][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:36.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:36.143][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:36.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:36.149][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:36.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:36.156][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:36.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:36.163][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:36.165][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:36.166][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:36.174][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:36.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:36.177][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:36.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:36.181][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:36.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:36.188][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:36.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:36.195][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:36.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:36.201][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:36.203][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:36.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:36.212][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:36.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:36.215][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:36.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:36.217][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:36.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:36.223][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:36.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:36.228][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:36.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:36.234][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:36.235][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:36.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:36.242][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:36.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:36.245][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:36.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:36.248][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:36.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:36.254][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:36.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:36.259][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:36.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:36.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:36.292][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-04-17 04:29:36.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-04-17 04:29:36.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:36.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-17 04:29:36.307][biodb::testThat]
biodb.INFO [2025-04-17 04:29:36.309][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-04-17 04:29:36.310][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-17 04:29:36.311][biodb::testThat]
biodb.TRACE[2025-04-17 04:29:36.316][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-17 04:29:36.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-17 04:29:36.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:36.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:36.321][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:36.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:36.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:36.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:36.327][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:36.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:36.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:36.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:36.332][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:36.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:36.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:36.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:36.338][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:36.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:36.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:36.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:36.347][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:36.349][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:36.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:36.356][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:36.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:36.359][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:36.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:36.364][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-17 04:29:36.369][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:29:36.370][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:29:36.373][private$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[2025-04-17 04:29:37.098][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[2025-04-17 04:29:37.851][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:29:37.854][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-04-17 04:29:37.860][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-04-17 04:29:37.864][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:37.866][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:37.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:37.874][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:37.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:37.876][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:37.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:37.879][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:37.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:37.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:37.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:37.885][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:37.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:37.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:37.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:37.890][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:37.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:37.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:37.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:37.897][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[2025-04-17 04:29:37.902][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:29:37.903][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:29:37.906][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-17 04:29:38.658][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-17 04:29:39.484][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:29:39.487][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-04-17 04:29:39.492][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-04-17 04:29:39.496][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:39.498][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:39.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:39.506][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:39.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:39.508][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:39.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:39.511][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:39.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:39.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:39.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:39.517][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:39.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:39.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:39.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:39.522][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:39.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:39.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:39.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:39.528][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:39.529][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:39.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:39.537][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:39.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:39.539][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:39.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:39.542][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:39.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:39.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:39.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:39.549][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:39.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:39.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:39.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:39.555][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:39.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:39.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:39.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:39.561][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-04-17 04:29:39.563][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:39.565][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:39.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:39.573][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:39.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:39.576][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:39.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:39.579][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:39.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:39.586][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:39.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:39.592][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:39.594][private$selectFields]
biodb.TRACE[2025-04-17 04:29:39.595][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-17 04:29:39.616][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-17 04:29:39.618][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:39.619][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.621][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.623][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:39.624][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:39.626][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.627][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.629][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:39.630][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:39.631][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:39.633][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:39.634][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.636][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.637][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:39.638][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:39.640][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-17 04:29:39.641][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:39.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:39.647][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:39.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:39.653][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:39.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:39.675][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-04-17 04:29:39.676][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:39.678][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:39.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:39.685][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:39.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:39.688][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:39.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:39.691][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:39.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:39.697][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:39.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:39.703][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:39.704][private$selectFields]
biodb.TRACE[2025-04-17 04:29:39.706][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-17 04:29:39.707][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-17 04:29:39.709][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:39.710][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.712][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.714][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:39.715][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:39.717][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.718][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.720][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:39.721][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:39.722][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:39.724][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:39.725][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.727][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.728][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:39.729][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:39.731][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-17 04:29:39.732][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:39.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:39.738][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:39.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:39.744][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:39.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:39.751][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-04-17 04:29:39.752][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:39.754][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:39.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:39.762][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:39.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:39.765][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:39.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:39.768][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:39.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:39.774][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:39.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:39.780][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:39.782][private$selectFields]
biodb.TRACE[2025-04-17 04:29:39.783][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-17 04:29:39.785][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-17 04:29:39.786][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:39.788][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.790][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.791][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:39.793][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:39.794][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.796][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.798][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:39.799][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:39.801][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:39.802][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:39.804][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.806][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.807][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:39.809][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:39.811][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-17 04:29:39.812][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:39.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:39.818][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:39.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:39.824][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:39.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:39.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:39.830][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-04-17 04:29:39.832][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-04-17 04:29:39.833][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-04-17 04:29:39.848][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:39.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:39.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:39.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:39.854][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:39.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:39.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:39.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:39.860][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:39.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:39.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:39.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:39.867][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:39.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:39.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:39.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:40.043][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:40.047][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:40.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:40.064][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:40.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:40.069][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:40.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:40.079][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-17 04:29:40.089][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:29:40.091][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:29:40.096][private$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[2025-04-17 04:29:40.853][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[2025-04-17 04:29:41.585][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:29:41.588][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2025-04-17 04:29:41.594][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2025-04-17 04:29:41.600][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[2025-04-17 04:29:41.605][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:29:41.606][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:29:41.609][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-17 04:29:42.396][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-17 04:29:43.146][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:29:43.150][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2025-04-17 04:29:43.156][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2025-04-17 04:29:43.162][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:43.163][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:43.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:43.172][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:43.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:43.175][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:43.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:43.179][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:43.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:43.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.185][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:43.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:43.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.191][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:43.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:43.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:43.198][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:43.199][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:43.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:43.208][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:43.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:43.211][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:43.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:43.214][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:43.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:43.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.220][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:43.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:43.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.226][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:43.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:43.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:43.231][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:43.233][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:43.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:43.241][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:43.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:43.244][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:43.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:43.247][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:43.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:43.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.253][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:43.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:43.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.259][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:43.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:43.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:43.329][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-04-17 04:29:43.366][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:43.368][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:43.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:43.376][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:43.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:43.378][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:43.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:43.381][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.387][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.392][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:43.394][private$selectFields]
biodb.TRACE[2025-04-17 04:29:43.395][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-17 04:29:43.396][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-17 04:29:43.398][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:43.399][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.400][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.402][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.403][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.404][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.406][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.407][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.408][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.410][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:43.411][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:43.412][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.414][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.415][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.417][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.418][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-17 04:29:43.419][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.425][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.430][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.436][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-04-17 04:29:43.438][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:43.439][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:43.440][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:43.446][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:43.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:43.449][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:43.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:43.470][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.476][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.522][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:43.524][private$selectFields]
biodb.TRACE[2025-04-17 04:29:43.525][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-17 04:29:43.526][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-17 04:29:43.528][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:43.529][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.531][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.532][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.533][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.535][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.536][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.537][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.539][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.540][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:43.557][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:43.558][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.560][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.561][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.563][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.565][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-17 04:29:43.567][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.573][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.579][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.585][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-04-17 04:29:43.586][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:43.588][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:43.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:43.596][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:43.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:43.599][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:43.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:43.602][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.608][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.614][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:43.616][private$selectFields]
biodb.TRACE[2025-04-17 04:29:43.617][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-17 04:29:43.619][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-17 04:29:43.620][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:43.622][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.623][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.625][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.626][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.628][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.630][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.631][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.633][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.634][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:43.636][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:43.637][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.639][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.640][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.642][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.643][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-17 04:29:43.645][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.650][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.656][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.662][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-04-17 04:29:43.663][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-04-17 04:29:43.664][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-04-17 04:29:43.677][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-04-17 04:29:43.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-04-17 04:29:43.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-17 04:29:43.687][biodb::testThat]
biodb.INFO [2025-04-17 04:29:43.689][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-04-17 04:29:43.690][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-17 04:29:43.691][biodb::testThat]
biodb.TRACE[2025-04-17 04:29:43.696][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-17 04:29:43.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-17 04:29:43.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.702][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:43.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:43.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.708][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:43.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:43.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.713][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:43.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:43.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.720][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:43.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:43.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:43.730][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:43.731][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:43.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:43.739][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:43.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:43.742][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:43.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:43.747][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-17 04:29:43.752][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-17 04:29:43.754][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-04-17 04:29:43.756][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-17 04:29:43.759][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-04-17 04:29:43.762][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:43.763][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:43.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:43.772][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:43.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:43.775][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:43.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:43.778][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:43.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:43.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.794][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:43.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:43.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.800][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:43.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:43.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:43.807][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-17 04:29:43.812][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-17 04:29:43.814][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-04-17 04:29:43.815][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-17 04:29:43.817][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-04-17 04:29:43.821][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:43.822][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:43.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:43.830][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:43.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:43.833][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:43.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:43.836][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:43.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:43.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.842][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:43.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:43.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.848][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:43.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:43.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:43.853][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:43.855][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:43.856][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:43.863][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:43.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:43.865][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:43.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:43.868][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:43.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:43.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.874][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:43.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:43.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.880][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:43.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:43.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:43.887][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-04-17 04:29:43.889][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:43.891][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:43.892][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:43.899][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:43.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:43.902][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:43.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:43.905][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.912][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.918][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:43.919][private$selectFields]
biodb.TRACE[2025-04-17 04:29:43.920][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-17 04:29:43.922][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-17 04:29:43.923][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:43.925][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.926][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.928][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.929][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.931][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.932][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.934][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.935][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.937][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:43.938][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:43.940][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.941][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.943][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.944][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.946][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-17 04:29:43.947][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.954][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.961][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:43.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:43.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:43.968][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-04-17 04:29:43.970][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:43.971][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:43.983][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:44.001][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:44.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:44.004][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:44.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:44.009][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.017][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.024][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:44.026][private$selectFields]
biodb.TRACE[2025-04-17 04:29:44.028][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-17 04:29:44.030][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-17 04:29:44.031][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:44.033][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.036][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.037][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.039][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.041][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.042][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.044][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.046][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.047][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:44.049][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:44.051][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.053][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.054][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.056][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.057][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-17 04:29:44.059][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.066][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.072][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.080][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-04-17 04:29:44.082][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:44.084][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:44.085][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:44.093][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:44.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:44.126][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:44.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:44.133][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.142][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.149][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:44.151][private$selectFields]
biodb.TRACE[2025-04-17 04:29:44.153][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-17 04:29:44.155][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-17 04:29:44.157][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:44.159][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.161][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.163][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.165][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.167][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.169][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.171][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.173][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.175][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:44.177][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:44.179][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.182][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.183][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.186][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.187][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-17 04:29:44.189][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.197][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.207][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.215][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-04-17 04:29:44.216][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-04-17 04:29:44.218][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-04-17 04:29:44.233][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:44.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:44.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.241][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:44.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:44.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.248][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:44.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:44.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.255][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:44.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:44.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:44.267][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:44.268][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:44.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:44.278][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:44.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:44.281][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:44.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:44.287][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-17 04:29:44.293][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-17 04:29:44.295][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-04-17 04:29:44.297][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-17 04:29:44.298][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-04-17 04:29:44.303][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-17 04:29:44.308][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-17 04:29:44.310][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-04-17 04:29:44.312][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-17 04:29:44.314][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-04-17 04:29:44.318][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:44.319][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:44.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:44.327][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:44.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:44.330][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:44.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:44.333][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:44.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:44.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.339][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:44.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:44.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.344][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:44.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:44.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:44.350][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:44.351][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:44.352][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:44.359][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:44.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:44.361][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:44.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:44.364][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:44.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:44.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.370][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:44.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:44.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.376][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:44.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:44.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:44.381][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:44.382][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:44.384][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:44.391][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:44.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:44.393][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:44.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:44.396][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:44.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:44.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.402][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:44.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:44.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.407][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:44.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:44.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:44.413][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-04-17 04:29:44.415][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:44.416][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:44.417][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:44.432][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:44.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:44.435][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:44.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:44.439][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.444][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.449][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:44.451][private$selectFields]
biodb.TRACE[2025-04-17 04:29:44.452][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-17 04:29:44.453][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-17 04:29:44.455][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:44.456][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.458][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.459][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.460][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.462][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.463][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.464][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.466][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.467][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:44.468][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:44.470][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.471][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.472][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.474][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.475][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-17 04:29:44.476][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.482][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.487][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.493][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-04-17 04:29:44.494][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:44.495][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:44.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:44.503][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:44.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:44.505][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:44.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:44.508][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.514][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.519][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:44.520][private$selectFields]
biodb.TRACE[2025-04-17 04:29:44.522][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-17 04:29:44.523][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-17 04:29:44.524][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:44.526][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.527][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.528][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.530][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.531][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.533][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.534][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.535][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.537][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:44.539][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:44.540][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.541][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.543][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.544][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.546][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-17 04:29:44.547][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.553][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.559][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.565][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-04-17 04:29:44.567][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:44.568][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:44.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:44.576][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:44.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:44.578][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:44.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:44.581][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.586][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.593][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:44.594][private$selectFields]
biodb.TRACE[2025-04-17 04:29:44.596][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-17 04:29:44.597][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-17 04:29:44.598][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:44.600][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.601][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.602][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.604][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.605][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.607][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.608][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.609][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.610][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:44.612][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:44.613][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.615][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.616][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.618][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.619][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-17 04:29:44.621][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.627][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.633][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.639][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-04-17 04:29:44.640][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-04-17 04:29:44.642][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-04-17 04:29:44.654][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-04-17 04:29:44.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-04-17 04:29:44.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-17 04:29:44.665][biodb::testThat]
biodb.INFO [2025-04-17 04:29:44.666][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-04-17 04:29:44.667][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-17 04:29:44.669][biodb::testThat]
biodb.TRACE[2025-04-17 04:29:44.673][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-17 04:29:44.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-17 04:29:44.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.679][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:44.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:44.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.694][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:44.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:44.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.700][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:44.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:44.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.705][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:44.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:44.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:44.717][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:44.718][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:44.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:44.726][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:44.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:44.728][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:44.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:44.734][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-17 04:29:44.738][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-17 04:29:44.740][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-04-17 04:29:44.742][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-17 04:29:44.744][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-04-17 04:29:44.747][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:44.748][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:44.750][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:44.756][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:44.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:44.759][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:44.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:44.762][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:44.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:44.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.768][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:44.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:44.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.773][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:44.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:44.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:44.780][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-17 04:29:44.785][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-17 04:29:44.787][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-04-17 04:29:44.789][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-17 04:29:44.791][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-04-17 04:29:44.794][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:44.796][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:44.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:44.804][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:44.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:44.807][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:44.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:44.810][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:44.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:44.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.816][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:44.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:44.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.822][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:44.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:44.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:44.828][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:44.829][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:44.830][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:44.836][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:44.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:44.839][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:44.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:44.842][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:44.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:44.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.847][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:44.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:44.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.853][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:44.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:44.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:44.859][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-04-17 04:29:44.861][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:44.862][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:44.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:44.870][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:44.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:44.872][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:44.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:44.875][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.881][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.886][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:44.888][private$selectFields]
biodb.TRACE[2025-04-17 04:29:44.889][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-17 04:29:44.890][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-17 04:29:44.892][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:44.893][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.895][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.896][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.897][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.899][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.900][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.901][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.903][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.904][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:44.906][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:44.907][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.908][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.910][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.911][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.912][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-17 04:29:44.914][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.919][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.925][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.931][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-04-17 04:29:44.932][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:44.934][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:44.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:44.950][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:44.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:44.953][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:44.955][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.TRACE[2025-04-17 04:29:44.956][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.962][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.968][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:44.969][private$selectFields]
biodb.TRACE[2025-04-17 04:29:44.970][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-17 04:29:44.972][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-17 04:29:44.973][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:44.974][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.976][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.977][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.978][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.980][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.981][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.983][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.984][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.985][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:44.987][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:44.988][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.990][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.991][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:44.992][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:44.993][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-17 04:29:44.995][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:44.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.001][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.006][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.012][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-04-17 04:29:45.014][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:45.015][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:45.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:45.022][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:45.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:45.025][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:45.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:45.028][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.034][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.039][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:45.041][private$selectFields]
biodb.TRACE[2025-04-17 04:29:45.042][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-17 04:29:45.044][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-17 04:29:45.045][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:45.047][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.048][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.050][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.051][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.053][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.054][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.056][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.057][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.058][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:45.060][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:45.061][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.063][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.064][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.065][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.066][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-17 04:29:45.068][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.074][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.079][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.085][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-04-17 04:29:45.086][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-04-17 04:29:45.088][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-04-17 04:29:45.115][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:45.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:45.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.120][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:45.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:45.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.126][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:45.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:45.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.131][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:45.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:45.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:45.142][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:45.143][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:45.144][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:45.151][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:45.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:45.153][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:45.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:45.158][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-17 04:29:45.163][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-17 04:29:45.165][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-04-17 04:29:45.166][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-17 04:29:45.168][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-04-17 04:29:45.172][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-17 04:29:45.177][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-17 04:29:45.179][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-04-17 04:29:45.180][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-17 04:29:45.182][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-04-17 04:29:45.186][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:45.187][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:45.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:45.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:45.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:45.198][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:45.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:45.210][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:45.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:45.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.216][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:45.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:45.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.222][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:45.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:45.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:45.228][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:45.229][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:45.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:45.236][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:45.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:45.239][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:45.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:45.242][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:45.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:45.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.247][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:45.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:45.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.253][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:45.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:45.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:45.259][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:45.260][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:45.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:45.267][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:45.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:45.270][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:45.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:45.273][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:45.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:45.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.278][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:45.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:45.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.284][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:45.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:45.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:45.289][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-04-17 04:29:45.292][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:45.293][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:45.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:45.301][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:45.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:45.303][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:45.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:45.306][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.312][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.317][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:45.319][private$selectFields]
biodb.TRACE[2025-04-17 04:29:45.320][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-17 04:29:45.321][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-17 04:29:45.323][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:45.324][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.326][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.327][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.329][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.330][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.332][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.333][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.334][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.336][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:45.337][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:45.338][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.340][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.341][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.343][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.344][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-17 04:29:45.345][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.351][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.356][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.362][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-04-17 04:29:45.363][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:45.365][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:45.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:45.372][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:45.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:45.375][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:45.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:45.378][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.383][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.389][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:45.390][private$selectFields]
biodb.TRACE[2025-04-17 04:29:45.391][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-17 04:29:45.392][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-17 04:29:45.394][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:45.395][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.397][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.398][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.399][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.401][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.402][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.404][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.405][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.406][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:45.408][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:45.409][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.411][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.412][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.421][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.424][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-17 04:29:45.426][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.432][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.438][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.446][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-04-17 04:29:45.448][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:45.449][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:45.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:45.462][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:45.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:45.465][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:45.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:45.468][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.494][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.500][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:45.502][private$selectFields]
biodb.TRACE[2025-04-17 04:29:45.503][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-17 04:29:45.505][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-17 04:29:45.506][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:45.508][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.509][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.511][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.512][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.514][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.515][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.517][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.518][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.519][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:45.521][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-17 04:29:45.522][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.524][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.525][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.527][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.528][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-17 04:29:45.530][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.536][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.542][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:45.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:45.548][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-04-17 04:29:45.549][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-04-17 04:29:45.551][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-04-17 04:29:45.578][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-04-17 04:29:45.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-04-17 04:29:45.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:45.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-17 04:29:45.589][biodb::testThat]
biodb.INFO [2025-04-17 04:29:45.590][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2025-04-17 04:29:45.592][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-17 04:29:45.593][biodb::testThat]
biodb.DEBUG[2025-04-17 04:29:45.596][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-04-17 04:29:45.597][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-17 04:29:45.600][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-04-17 04:29:45.602][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-17 04:29:45.603][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-17 04:29:45.605][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-17 04:29:45.607][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-17 04:29:45.609][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-17 04:29:45.610][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-17 04:29:45.615][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:45.616][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:45.618][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:45.625][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:45.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:45.627][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:45.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:45.631][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2025-04-17 04:29:45.635][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:29:45.637][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:29:45.639][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2025-04-17 04:29:47.771][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2025-04-17 04:29:48.493][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:29:48.497][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2025-04-17 04:29:48.503][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2025-04-17 04:29:48.508][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2025-04-17 04:29:48.511][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-17 04:29:48.513][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-17 04:29:48.516][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-17 04:29:48.519][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:48.521][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:48.523][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:48.531][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:48.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:48.535][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:48.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:48.541][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:48.543][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:48.545][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:48.547][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:48.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:48.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:48.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:48.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:48.558][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:29:48.560][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:29:48.562][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:48.563][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:48.566][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:29:48.568][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:29:48.569][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:48.571][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:48.574][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:29:48.576][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:29:48.578][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:48.580][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:48.582][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:29:48.584][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:29:48.586][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:48.588][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:48.590][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:48.592][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:48.593][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:48.595][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:48.597][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:29:48.598][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:48.600][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:48.601][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:48.603][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:48.605][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:48.606][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:48.608][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:48.610][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:29:48.612][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:29:48.613][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:48.615][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:48.617][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:29:48.619][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:29:48.620][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:48.622][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:48.624][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:29:48.626][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:29:48.627][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:48.629][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:48.647][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:48.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:48.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:48.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:48.655][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:48.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:48.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:48.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:48.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:48.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:48.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:48.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:48.669][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:48.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:48.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:48.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:48.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:48.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:48.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:48.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:48.684][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:48.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:48.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:48.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:48.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:48.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:48.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:48.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:48.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:48.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:48.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:48.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:48.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:48.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:48.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:48.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:48.714][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:48.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:48.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:48.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:48.721][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-04-17 04:29:48.723][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-04-17 04:29:48.735][biodb::testThat]
biodb.INFO [2025-04-17 04:29:48.736][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-04-17 04:29:48.738][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-17 04:29:48.739][biodb::testThat]
biodb.DEBUG[2025-04-17 04:29:48.754][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-04-17 04:29:48.756][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-04-17 04:29:48.758][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2025-04-17 04:29:48.760][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2025-04-17 04:29:48.762][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2025-04-17 04:29:48.764][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-17 04:29:48.765][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-17 04:29:48.767][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-17 04:29:48.768][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-17 04:29:48.770][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-17 04:29:48.776][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:48.777][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:48.778][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:48.785][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:48.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:48.788][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:48.789][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[2025-04-17 04:29:48.791][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2025-04-17 04:29:48.795][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:29:48.796][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:29:48.799][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2025-04-17 04:29:49.516][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2025-04-17 04:29:50.239][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:29:50.242][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2025-04-17 04:29:50.247][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2025-04-17 04:29:50.249][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:50.250][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:50.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:50.258][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:50.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:50.260][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:50.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:50.263][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2025-04-17 04:29:50.267][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:29:50.268][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:29:50.270][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2025-04-17 04:29:50.994][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2025-04-17 04:29:53.099][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:29:53.102][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2025-04-17 04:29:53.106][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2025-04-17 04:29:53.108][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:53.110][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:53.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:53.117][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:53.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:53.120][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:53.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:53.123][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2025-04-17 04:29:53.127][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:29:53.129][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:29:53.131][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2025-04-17 04:29:53.852][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2025-04-17 04:29:54.573][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:29:54.575][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2025-04-17 04:29:54.580][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2025-04-17 04:29:54.584][private$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[2025-04-17 04:29:54.586][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-17 04:29:54.587][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-04-17 04:29:54.589][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-04-17 04:29:54.591][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:54.593][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:54.594][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:54.600][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:54.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:54.603][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:54.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:54.607][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:54.609][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:54.610][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.611][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:54.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:54.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.641][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:29:54.643][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:29:54.644][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.646][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.647][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:29:54.649][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:29:54.650][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.652][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.654][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:29:54.655][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:29:54.657][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.658][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.660][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:29:54.661][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:29:54.663][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.664][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.666][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:54.667][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:54.669][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.670][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.672][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:29:54.673][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:54.675][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.676][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.678][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:54.679][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:54.680][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.682][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.683][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:29:54.685][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:29:54.686][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.688][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.690][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:29:54.691][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:29:54.692][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.694][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.695][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:29:54.697][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:29:54.698][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.700][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.702][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:54.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:54.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.707][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:54.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:54.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:54.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:54.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.718][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:54.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:54.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:54.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:54.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:54.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:54.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:54.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:54.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:54.741][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:54.742][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:54.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:54.750][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:54.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:54.752][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:54.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:54.756][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:54.758][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:54.759][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.761][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:54.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:54.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.768][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:29:54.770][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:29:54.771][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.772][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.774][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:29:54.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:29:54.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.780][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:29:54.781][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:29:54.782][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.784][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.786][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:29:54.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:29:54.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.792][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:29:54.793][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:29:54.795][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.796][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.798][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:29:54.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:29:54.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.804][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:29:54.805][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:29:54.807][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.808][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.810][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:29:54.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:29:54.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.816][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:54.817][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:54.819][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.820][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.822][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:54.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:54.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.828][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:29:54.830][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:54.831][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.832][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.834][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:29:54.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:54.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.840][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:54.842][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:54.843][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.845][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.846][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:54.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:54.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.852][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:29:54.854][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:29:54.855][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.856][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.858][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:29:54.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:29:54.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.864][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:29:54.866][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:29:54.867][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.869][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.870][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:29:54.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:29:54.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.876][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:29:54.878][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:29:54.879][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.881][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.882][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:29:54.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:29:54.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.897][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:54.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:54.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.904][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:54.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:54.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:54.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:54.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.916][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:54.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:54.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:54.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:54.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:54.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:54.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:54.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:54.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:54.940][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:29:54.941][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:54.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:54.949][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:54.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:54.951][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:54.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-17 04:29:54.964][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:54.966][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:54.968][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.969][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:54.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:54.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.977][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:29:54.979][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:29:54.981][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.982][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.984][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:29:54.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:29:54.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.990][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:29:54.992][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:29:54.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:54.995][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:54.997][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:29:54.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:29:55.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:55.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:55.004][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:29:55.005][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:29:55.007][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:55.008][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:55.011][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:29:55.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:29:55.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:55.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:55.017][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:29:55.019][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:29:55.020][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:55.022][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:55.024][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:29:55.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:29:55.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:55.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:55.030][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:55.032][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:55.033][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:55.035][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:55.037][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:55.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:29:55.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:55.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:55.043][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:29:55.045][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:55.046][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:55.048][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:55.050][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:29:55.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:29:55.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:55.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:55.056][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:55.058][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:55.059][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:55.061][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:55.063][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:55.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:55.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:55.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:55.069][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:29:55.071][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:29:55.073][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:55.074][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:55.077][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:29:55.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:29:55.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:55.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:55.083][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:29:55.085][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:29:55.086][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:55.088][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:55.090][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:29:55.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:29:55.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:55.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:55.097][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:29:55.099][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:29:55.100][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:55.102][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:55.104][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:29:55.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:29:55.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:55.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:55.111][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:55.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:55.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:55.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:55.117][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:55.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:55.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:55.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:55.123][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:55.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:55.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:55.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:55.130][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:29:55.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:29:55.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:55.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:55.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:55.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:55.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:55.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:55.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:55.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:55.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:55.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:55.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:55.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:55.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:55.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:55.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:55.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:55.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:55.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:55.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:55.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:55.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:55.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:55.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:55.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:55.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:55.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:55.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:55.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:55.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:55.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:55.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:55.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:55.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:55.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:55.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:55.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:55.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:55.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:55.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:55.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:55.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:55.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:55.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:55.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:55.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:55.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:55.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:29:55.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:29:55.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:55.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:29:55.232][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-04-17 04:29:55.233][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-04-17 04:29:55.235][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2025-04-17 04:29:55.255][biodb::testThat]
biodb.INFO [2025-04-17 04:29:55.256][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2025-04-17 04:29:55.258][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-17 04:29:55.259][biodb::testThat]
biodb.INFO [2025-04-17 04:29:55.295][biodb::testThat]
biodb.INFO [2025-04-17 04:29:55.297][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2025-04-17 04:29:55.298][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-17 04:29:55.300][biodb::testThat]
biodb.INFO [2025-04-17 04:29:55.312][biodb::testThat]
biodb.INFO [2025-04-17 04:29:55.313][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2025-04-17 04:29:55.315][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-17 04:29:55.316][biodb::testThat]
biodb.DEBUG[2025-04-17 04:29:55.320][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2025-04-17 04:29:55.325][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:29:55.326][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:29:55.329][private$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[2025-04-17 04:29:56.160][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[2025-04-17 04:29:57.002][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:29:57.005][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2025-04-17 04:29:57.010][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2025-04-17 04:29:57.027][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:29:57.029][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:29:57.030][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:57.032][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:29:57.033][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:57.034][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:29:57.036][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:29:57.037][ef$get] fields variable is a list.
biodb.INFO [2025-04-17 04:29:57.039][biodb::testThat]
biodb.INFO [2025-04-17 04:29:57.041][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2025-04-17 04:29:57.042][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-17 04:29:57.043][biodb::testThat]
biodb.ERROR[2025-04-17 04:29:57.063][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-04-17 04:29:57.087][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-04-17 04:29:57.104][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-17 04:29:57.106][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-04-17 04:29:57.108][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-04-17 04:29:57.109][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-17 04:29:57.110][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:57.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:57.113][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:57.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:57.115][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.117][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.INFO [2025-04-17 04:29:57.146][biodb::testContext]
biodb.INFO [2025-04-17 04:29:57.147][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-17 04:29:57.149][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-04-17 04:29:57.150][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-17 04:29:57.152][biodb::testContext]
biodb.INFO [2025-04-17 04:29:57.155][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-04-17 04:29:57.157][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-devel_2025-02-19/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-04-17 04:29:57.162][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-17 04:29:57.164][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-17 04:29:57.165][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-17 04:29:57.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:57.171][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-17 04:29:57.172][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-17 04:29:57.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:57.178][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-17 04:29:57.179][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-17 04:29:57.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:57.185][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-17 04:29:57.186][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-17 04:29:57.188][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-17 04:29:57.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:57.193][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-17 04:29:57.195][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-17 04:29:57.196][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-17 04:29:57.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:57.202][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-17 04:29:57.203][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-17 04:29:57.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:57.209][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-17 04:29:57.210][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-17 04:29:57.212][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-17 04:29:57.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:57.217][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-17 04:29:57.219][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-17 04:29:57.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.223][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[2025-04-17 04:29:57.224][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-17 04:29:57.226][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-17 04:29:57.227][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-17 04:29:57.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:57.233][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-17 04:29:57.234][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-17 04:29:57.236][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-17 04:29:57.237][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-17 04:29:57.239][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-17 04:29:57.240][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-17 04:29:57.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.244][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[2025-04-17 04:29:57.246][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-17 04:29:57.247][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-17 04:29:57.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:57.253][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-17 04:29:57.254][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-17 04:29:57.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.258][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[2025-04-17 04:29:57.259][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-17 04:29:57.261][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-17 04:29:57.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:57.266][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-17 04:29:57.268][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-17 04:29:57.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:57.273][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-17 04:29:57.275][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-17 04:29:57.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:57.280][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-17 04:29:57.282][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-17 04:29:57.287][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-17 04:29:57.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:57.292][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-17 04:29:57.294][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-17 04:29:57.296][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-17 04:29:57.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:57.301][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-17 04:29:57.304][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-17 04:29:57.306][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-04-17 04:29:57.307][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-17 04:29:57.309][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-17 04:29:57.311][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-17 04:29:57.312][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-17 04:29:57.314][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-17 04:29:57.315][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-17 04:29:57.317][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-17 04:29:57.318][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-17 04:29:57.320][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-17 04:29:57.321][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-17 04:29:57.323][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-17 04:29:57.324][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:29:57.326][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-17 04:29:57.327][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-17 04:29:57.327][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-17 04:29:57.327][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-17 04:29:57.327][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-17 04:29:57.327][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-17 04:29:57.329][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-17 04:29:57.330][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:29:57.332][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:29:57.333][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-17 04:29:57.335][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:29:57.336][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:29:57.337][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-17 04:29:57.339][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:29:57.340][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-17 04:29:57.342][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-17 04:29:57.343][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-17 04:29:57.345][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:29:57.347][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-17 04:29:57.350][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-17 04:29:57.352][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-17 04:29:57.353][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-17 04:29:57.355][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-17 04:29:57.356][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-17 04:29:57.358][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-17 04:29:57.360][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-17 04:29:57.361][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-17 04:29:57.363][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-17 04:29:57.364][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-17 04:29:57.366][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-17 04:29:57.368][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-17 04:29:57.369][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-17 04:29:57.371][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:29:57.372][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-17 04:29:57.374][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-17 04:29:57.374][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-17 04:29:57.374][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-17 04:29:57.374][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-17 04:29:57.374][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-17 04:29:57.376][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-17 04:29:57.377][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:29:57.379][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:29:57.380][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-17 04:29:57.382][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:29:57.383][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:29:57.385][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-17 04:29:57.386][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:29:57.388][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-17 04:29:57.390][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-17 04:29:57.391][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-17 04:29:57.402][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:29:57.404][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-17 04:29:57.407][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-17 04:29:57.408][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-04-17 04:29:57.410][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-17 04:29:57.411][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-17 04:29:57.413][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-17 04:29:57.414][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-17 04:29:57.415][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-17 04:29:57.417][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-17 04:29:57.418][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-17 04:29:57.420][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-17 04:29:57.421][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-17 04:29:57.422][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-17 04:29:57.424][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-17 04:29:57.425][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:29:57.427][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-17 04:29:57.428][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:29:57.429][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-17 04:29:57.431][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:29:57.432][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:29:57.433][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-17 04:29:57.434][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:29:57.436][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:29:57.437][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-17 04:29:57.438][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:29:57.440][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-17 04:29:57.441][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-17 04:29:57.442][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-17 04:29:57.444][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:29:57.445][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-17 04:29:57.448][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-17 04:29:57.449][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-17 04:29:57.450][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-17 04:29:57.452][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-17 04:29:57.453][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-17 04:29:57.454][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-17 04:29:57.456][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-17 04:29:57.457][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-17 04:29:57.458][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-17 04:29:57.460][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-17 04:29:57.461][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-17 04:29:57.463][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-17 04:29:57.464][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-17 04:29:57.465][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:29:57.467][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-17 04:29:57.468][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:29:57.469][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-17 04:29:57.471][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:29:57.472][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:29:57.473][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-17 04:29:57.475][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:29:57.476][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:29:57.477][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-17 04:29:57.479][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:29:57.480][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-17 04:29:57.481][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-17 04:29:57.482][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-17 04:29:57.484][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:29:57.486][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-17 04:29:57.487][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.488][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[2025-04-17 04:29:57.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:57.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:57.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:57.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:57.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:57.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.500][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[2025-04-17 04:29:57.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:57.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:57.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:57.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:57.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:57.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:57.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:57.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:57.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:57.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:57.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:57.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.525][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[2025-04-17 04:29:57.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:57.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:57.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.531][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[2025-04-17 04:29:57.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:57.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:57.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:57.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:57.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:57.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.544][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.DEBUG[2025-04-17 04:29:57.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:57.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:57.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:57.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:57.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:57.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:57.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:57.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:57.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:57.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:57.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:57.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.570][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[2025-04-17 04:29:57.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:57.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:57.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:57.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:57.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:57.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:57.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:57.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:57.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.589][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[2025-04-17 04:29:57.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:57.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:57.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:57.597][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-17 04:29:57.599][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-17 04:29:57.601][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-17 04:29:57.604][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-17 04:29:57.606][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-17 04:29:57.608][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-17 04:29:57.610][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-17 04:29:57.612][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-17 04:29:57.614][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-17 04:29:57.616][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-17 04:29:57.618][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-17 04:29:57.620][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-17 04:29:57.622][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-17 04:29:57.624][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-17 04:29:57.626][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-17 04:29:57.628][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-17 04:29:57.630][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-17 04:29:57.632][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-17 04:29:57.634][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-17 04:29:57.645][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-17 04:29:57.647][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-17 04:29:57.650][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-17 04:29:57.652][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-17 04:29:57.654][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-17 04:29:57.656][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-17 04:29:57.658][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-17 04:29:57.660][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-17 04:29:57.662][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-17 04:29:57.664][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-17 04:29:57.666][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-17 04:29:57.668][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-17 04:29:57.670][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-17 04:29:57.672][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-17 04:29:57.674][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-17 04:29:57.676][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-17 04:29:57.678][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-17 04:29:57.680][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-17 04:29:57.682][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-17 04:29:57.684][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-17 04:29:57.686][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-17 04:29:57.688][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-17 04:29:57.690][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-17 04:29:57.692][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-17 04:29:57.694][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-17 04:29:57.696][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-17 04:29:57.698][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-17 04:29:57.700][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-17 04:29:57.702][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-17 04:29:57.704][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-17 04:29:57.706][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-17 04:29:57.708][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-17 04:29:57.710][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-17 04:29:57.712][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-17 04:29:57.714][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-17 04:29:57.716][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-17 04:29:57.718][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-17 04:29:57.720][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-17 04:29:57.722][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-17 04:29:57.724][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-17 04:29:57.726][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-17 04:29:57.728][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-17 04:29:57.730][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-17 04:29:57.732][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-17 04:29:57.734][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-17 04:29:57.736][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-17 04:29:57.738][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-17 04:29:57.740][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-17 04:29:57.742][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-17 04:29:57.743][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-17 04:29:57.745][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-17 04:29:57.747][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-17 04:29:57.750][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-17 04:29:57.752][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-17 04:29:57.754][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-17 04:29:57.756][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-17 04:29:57.758][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-17 04:29:57.760][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-17 04:29:57.762][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-17 04:29:57.764][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-17 04:29:57.766][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-17 04:29:57.768][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-17 04:29:57.770][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-17 04:29:57.772][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-17 04:29:57.774][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-17 04:29:57.776][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-04-17 04:29:57.778][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-17 04:29:57.779][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:57.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:57.782][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.783][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.DEBUG[2025-04-17 04:29:57.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:57.787][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:57.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:57.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:57.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:57.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:57.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:57.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:57.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:57.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:57.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:57.805][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:57.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:57.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:57.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:57.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:57.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:57.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:57.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:57.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:57.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:57.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:57.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:57.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:57.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:57.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:57.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:57.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:57.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:57.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.836][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[2025-04-17 04:29:57.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:57.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:57.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:57.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:57.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.845][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[2025-04-17 04:29:57.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:57.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:57.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:57.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:57.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:57.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:57.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:57.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:57.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:57.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:57.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:57.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:57.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:57.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:57.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:57.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:57.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:57.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:57.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:57.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:58.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:58.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:58.165][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[2025-04-17 04:29:58.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:58.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:58.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:58.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:58.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:58.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:58.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:58.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:58.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:58.177][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:58.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:58.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:58.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:58.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:58.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:58.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:58.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:58.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:58.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:58.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:58.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:58.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:58.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:58.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:58.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:58.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:58.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:58.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:58.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:58.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:58.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:58.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:58.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:58.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:58.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:29:58.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:29:58.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:29:58.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:29:58.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:29:58.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:29:58.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:29:58.214][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[2025-04-17 04:29:58.216][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-devel_2025-02-19/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-04-17 04:29:58.217][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-04-17 04:29:58.220][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-17 04:29:58.221][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-04-17 04:29:58.223][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-17 04:29:58.224][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-17 04:29:58.225][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-17 04:29:58.227][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-17 04:29:58.228][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-17 04:29:58.229][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-04-17 04:29:58.230][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-17 04:29:58.232][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-17 04:29:58.233][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-17 04:29:58.234][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-04-17 04:29:58.236][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-17 04:29:58.237][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-04-17 04:29:58.237][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-04-17 04:29:58.237][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-04-17 04:29:58.237][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-04-17 04:29:58.237][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-04-17 04:29:58.237][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-04-17 04:29:58.237][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-04-17 04:29:58.237][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-04-17 04:29:58.237][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-04-17 04:29:58.237][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-04-17 04:29:58.237][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-04-17 04:29:58.238][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-17 04:29:58.240][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-17 04:29:58.240][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-17 04:29:58.240][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-17 04:29:58.241][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-17 04:29:58.242][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:29:58.243][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:29:58.245][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-17 04:29:58.246][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:29:58.247][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:29:58.248][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-17 04:29:58.250][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-17 04:29:58.250][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-04-17 04:29:58.251][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-17 04:29:58.252][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-17 04:29:58.253][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-17 04:29:58.255][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-04-17 04:29:58.255][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-04-17 04:29:58.257][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-17 04:29:58.259][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-17 04:29:58.261][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-04-17 04:29:58.263][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-17 04:29:58.265][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-17 04:29:58.267][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-17 04:29:58.271][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-04-17 04:29:58.273][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-04-17 04:29:58.275][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-04-17 04:29:58.277][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-04-17 04:29:58.278][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-17 04:29:58.280][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-17 04:29:58.282][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-04-17 04:29:58.283][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-04-17 04:29:58.285][biodb::testThat]
biodb.INFO [2025-04-17 04:29:58.286][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2025-04-17 04:29:58.287][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-17 04:29:58.289][biodb::testThat]
biodb.DEBUG[2025-04-17 04:29:58.294][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-04-17 04:29:58.299][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:29:58.300][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:29:58.302][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2025-04-17 04:29:59.028][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2025-04-17 04:29:59.967][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:29:59.970][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2025-04-17 04:29:59.975][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2025-04-17 04:29:59.980][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-17 04:29:59.985][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:29:59.987][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:29:59.989][private$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[2025-04-17 04:30:00.723][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[2025-04-17 04:30:01.558][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:30:01.561][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2025-04-17 04:30:01.567][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2025-04-17 04:30:01.569][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:30:01.571][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:01.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:01.578][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:01.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:01.581][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:01.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:01.584][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[2025-04-17 04:30:01.589][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:30:01.590][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:30:01.592][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-04-17 04:30:02.317][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-04-17 04:30:04.168][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:30:04.171][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2025-04-17 04:30:04.176][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2025-04-17 04:30:04.178][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:30:04.180][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:04.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:04.187][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:04.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:04.190][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:04.191][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[2025-04-17 04:30:04.236][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:30:04.237][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:04.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:04.244][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:04.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:04.247][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:04.248][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[2025-04-17 04:30:04.255][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-17 04:30:04.260][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-17 04:30:04.262][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-04-17 04:30:04.263][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-17 04:30:04.265][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-04-17 04:30:04.267][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:30:04.269][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:04.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:04.276][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:04.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:04.279][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:04.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:04.283][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-17 04:30:04.287][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-17 04:30:04.310][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-04-17 04:30:04.312][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-17 04:30:04.314][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-04-17 04:30:04.316][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:30:04.318][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:04.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:04.325][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:04.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:04.328][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:04.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:04.331][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:30:04.332][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:04.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:04.339][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:04.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:04.342][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:04.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:04.348][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-17 04:30:04.353][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-17 04:30:04.354][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-04-17 04:30:04.356][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-17 04:30:04.358][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-04-17 04:30:04.360][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:30:04.361][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:04.362][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:04.369][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:04.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:04.371][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:04.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:04.375][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-17 04:30:04.379][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-17 04:30:04.381][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-04-17 04:30:04.383][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-17 04:30:04.384][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-04-17 04:30:04.387][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:30:04.388][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:04.389][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:04.395][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:04.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:04.398][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:04.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:04.402][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-17 04:30:04.406][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:30:04.408][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:30:04.410][private$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[2025-04-17 04:30:05.244][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[2025-04-17 04:30:06.977][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:30:06.980][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2025-04-17 04:30:06.985][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2025-04-17 04:30:06.988][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:30:06.990][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:06.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:06.997][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:06.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:07.000][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:07.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-04-17 04:30:07.011][biodb::testThat]
biodb.INFO [2025-04-17 04:30:07.012][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2025-04-17 04:30:07.014][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-17 04:30:07.015][biodb::testThat]
biodb.DEBUG[2025-04-17 04:30:07.020][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[2025-04-17 04:30:07.025][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:30:07.026][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:30:07.030][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-04-17 04:30:07.831][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-04-17 04:30:08.595][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:30:08.598][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2025-04-17 04:30:08.604][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2025-04-17 04:30:08.606][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:30:08.608][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:08.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:08.616][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:08.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:08.618][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:08.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:08.625][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-17 04:30:08.630][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:30:08.632][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:30:08.634][private$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[2025-04-17 04:30:11.518][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[2025-04-17 04:30:12.261][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:30:12.264][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2025-04-17 04:30:12.270][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2025-04-17 04:30:12.273][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:30:12.274][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:12.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:12.283][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:12.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:12.285][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.286][FUN] Functions in observer BiodbConfig: [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 [2025-04-17 04:30:12.293][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-17 04:30:12.295][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-04-17 04:30:12.296][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-04-17 04:30:12.298][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-17 04:30:12.299][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:12.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:12.301][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:12.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:12.304][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.305][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.INFO [2025-04-17 04:30:12.309][biodb::testContext]
biodb.INFO [2025-04-17 04:30:12.311][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-17 04:30:12.312][biodb::testContext] Test context - Test web services
biodb.INFO [2025-04-17 04:30:12.314][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-17 04:30:12.315][biodb::testContext]
biodb.INFO [2025-04-17 04:30:12.318][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-04-17 04:30:12.320][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-devel_2025-02-19/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-04-17 04:30:12.325][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-17 04:30:12.326][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-17 04:30:12.327][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-17 04:30:12.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:12.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:12.333][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-17 04:30:12.334][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-17 04:30:12.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:12.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:12.339][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-17 04:30:12.341][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-17 04:30:12.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:12.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:12.346][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-17 04:30:12.347][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-17 04:30:12.349][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-17 04:30:12.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:12.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:12.354][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-17 04:30:12.355][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-17 04:30:12.357][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-17 04:30:12.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:12.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:12.362][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-17 04:30:12.363][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-17 04:30:12.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:12.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:12.368][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-17 04:30:12.370][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-17 04:30:12.371][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-17 04:30:12.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:12.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:12.376][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-17 04:30:12.378][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-17 04:30:12.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:12.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:12.383][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-17 04:30:12.384][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-17 04:30:12.386][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-17 04:30:12.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:12.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:12.391][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-17 04:30:12.392][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-17 04:30:12.393][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-17 04:30:12.395][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-17 04:30:12.396][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-17 04:30:12.398][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-17 04:30:12.399][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:12.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:12.403][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-17 04:30:12.404][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-17 04:30:12.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:12.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:12.410][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-17 04:30:12.411][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-17 04:30:12.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:12.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:12.416][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-17 04:30:12.418][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-17 04:30:12.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:12.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:12.423][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-17 04:30:12.424][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-17 04:30:12.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:12.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:12.430][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-17 04:30:12.431][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-17 04:30:12.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:12.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:12.436][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-17 04:30:12.438][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-17 04:30:12.443][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-17 04:30:12.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:12.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.447][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[2025-04-17 04:30:12.448][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-17 04:30:12.450][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-17 04:30:12.451][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-17 04:30:12.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:12.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:12.456][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-17 04:30:12.459][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-17 04:30:12.460][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-04-17 04:30:12.462][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:12.463][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-17 04:30:12.465][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:12.466][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-17 04:30:12.467][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-17 04:30:12.503][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-17 04:30:12.505][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-17 04:30:12.507][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-17 04:30:12.508][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:12.510][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-17 04:30:12.511][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-17 04:30:12.513][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:30:12.514][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:12.516][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-17 04:30:12.516][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-17 04:30:12.516][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-17 04:30:12.516][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-17 04:30:12.516][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-17 04:30:12.517][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-17 04:30:12.519][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:30:12.520][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:30:12.521][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-17 04:30:12.523][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:30:12.524][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:30:12.525][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-17 04:30:12.527][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:30:12.528][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-17 04:30:12.530][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-17 04:30:12.531][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-17 04:30:12.533][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:30:12.534][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-17 04:30:12.537][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-17 04:30:12.539][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-17 04:30:12.540][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:12.542][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-17 04:30:12.543][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:12.545][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-17 04:30:12.546][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-17 04:30:12.548][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-17 04:30:12.549][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-17 04:30:12.551][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-17 04:30:12.552][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:12.554][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-17 04:30:12.555][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-17 04:30:12.557][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:30:12.558][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:12.560][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-17 04:30:12.560][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-17 04:30:12.560][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-17 04:30:12.560][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-17 04:30:12.560][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-17 04:30:12.561][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-17 04:30:12.563][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:30:12.564][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:30:12.566][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-17 04:30:12.567][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:30:12.569][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:30:12.570][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-17 04:30:12.572][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:30:12.573][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-17 04:30:12.574][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-17 04:30:12.576][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-17 04:30:12.577][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:30:12.579][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-17 04:30:12.582][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:12.583][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-04-17 04:30:12.585][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:12.586][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-17 04:30:12.588][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:12.589][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-17 04:30:12.591][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-17 04:30:12.592][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-17 04:30:12.594][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-17 04:30:12.595][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-17 04:30:12.597][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-17 04:30:12.598][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-17 04:30:12.600][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-17 04:30:12.601][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:30:12.603][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:12.604][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:30:12.606][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-17 04:30:12.607][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:30:12.609][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:30:12.610][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-17 04:30:12.611][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:30:12.613][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:30:12.614][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-17 04:30:12.616][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:30:12.617][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-17 04:30:12.619][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-17 04:30:12.620][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-17 04:30:12.622][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:30:12.623][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-17 04:30:12.626][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:12.628][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-17 04:30:12.629][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:12.631][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-17 04:30:12.632][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:12.634][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-17 04:30:12.635][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-17 04:30:12.637][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-17 04:30:12.638][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-17 04:30:12.640][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-17 04:30:12.641][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-17 04:30:12.643][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-17 04:30:12.644][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-17 04:30:12.646][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:30:12.647][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:12.649][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:30:12.650][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-17 04:30:12.652][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:30:12.653][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:30:12.655][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-17 04:30:12.656][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:30:12.657][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:30:12.659][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-17 04:30:12.660][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:30:12.662][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-17 04:30:12.663][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-17 04:30:12.665][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-17 04:30:12.666][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:30:12.668][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-17 04:30:12.669][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:12.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:12.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:12.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:12.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:12.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:12.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:12.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:12.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.685][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[2025-04-17 04:30:12.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:12.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:12.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:12.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:12.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:12.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:12.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:12.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:12.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:12.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:12.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:12.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.706][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[2025-04-17 04:30:12.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:12.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:12.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:12.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:12.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:12.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:12.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:12.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.720][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[2025-04-17 04:30:12.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:12.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:12.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:12.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.727][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.DEBUG[2025-04-17 04:30:12.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:12.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:12.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:12.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:12.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:12.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:12.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:12.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:12.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:12.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:12.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:12.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.747][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[2025-04-17 04:30:12.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:12.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:12.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:12.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:12.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:12.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:12.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:12.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:12.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:12.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:12.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:12.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:12.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:12.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:12.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:12.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:12.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:12.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:12.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:12.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:12.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:12.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:12.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:12.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:12.794][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-17 04:30:12.796][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-17 04:30:12.798][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-17 04:30:12.800][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-17 04:30:12.802][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-17 04:30:12.804][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-17 04:30:12.806][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-17 04:30:12.808][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-17 04:30:12.810][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-17 04:30:12.812][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-17 04:30:12.814][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-17 04:30:12.815][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-17 04:30:12.817][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-17 04:30:12.819][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-17 04:30:12.821][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-17 04:30:12.823][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-17 04:30:12.825][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-17 04:30:12.827][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-17 04:30:12.829][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-17 04:30:12.831][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-17 04:30:12.833][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-17 04:30:12.835][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-17 04:30:12.837][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-17 04:30:12.839][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-17 04:30:12.841][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-17 04:30:12.843][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-17 04:30:12.845][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-17 04:30:12.847][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-17 04:30:12.849][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-17 04:30:12.851][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-17 04:30:12.854][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-17 04:30:12.856][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-17 04:30:12.858][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-17 04:30:12.860][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-17 04:30:12.862][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-17 04:30:12.864][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-17 04:30:12.866][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-17 04:30:12.868][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-17 04:30:12.870][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-17 04:30:12.872][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-17 04:30:12.874][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-17 04:30:12.876][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-17 04:30:12.878][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-17 04:30:12.880][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-17 04:30:12.882][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-17 04:30:12.884][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-17 04:30:12.886][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-17 04:30:12.888][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-17 04:30:12.890][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-17 04:30:12.892][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-17 04:30:12.894][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-17 04:30:12.895][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-17 04:30:12.897][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-17 04:30:12.899][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-17 04:30:12.902][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-17 04:30:12.904][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-17 04:30:12.906][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-17 04:30:12.908][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-17 04:30:12.910][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-17 04:30:12.912][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-17 04:30:12.914][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-17 04:30:12.916][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-17 04:30:12.918][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-17 04:30:12.921][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-17 04:30:12.923][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-17 04:30:12.925][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-17 04:30:12.927][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-17 04:30:12.929][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-17 04:30:12.931][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-17 04:30:12.933][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-17 04:30:12.936][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-17 04:30:12.938][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-17 04:30:12.940][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-17 04:30:12.942][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-17 04:30:12.944][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-17 04:30:12.947][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-17 04:30:12.949][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-17 04:30:12.951][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-17 04:30:12.953][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-17 04:30:12.955][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-17 04:30:12.957][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-17 04:30:12.959][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-17 04:30:12.961][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-17 04:30:12.964][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-17 04:30:12.966][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-04-17 04:30:12.967][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-17 04:30:12.969][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:12.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:12.971][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.973][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[2025-04-17 04:30:12.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:12.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:12.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:12.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:12.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:12.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:12.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:12.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:12.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:12.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:12.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:12.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:12.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:12.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:12.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:12.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:12.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:12.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:12.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:13.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:13.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:13.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:13.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:13.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:13.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:13.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:13.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:13.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:13.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:13.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:13.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:13.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:13.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:13.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:13.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:13.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:13.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:13.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:13.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:13.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:13.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:13.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:13.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:13.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:13.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:13.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:13.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:13.045][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.DEBUG[2025-04-17 04:30:13.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:13.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:13.050][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:13.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:13.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:13.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:13.055][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[2025-04-17 04:30:13.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:13.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:13.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:13.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:13.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:13.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:13.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:13.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:13.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:13.068][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:13.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:13.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:13.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:13.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:13.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:13.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:13.077][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:13.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:13.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:13.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:13.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:13.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:13.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:13.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:13.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:13.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:13.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:13.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:13.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:13.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:13.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:13.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:13.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:13.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:13.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:13.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:13.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:13.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:13.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:13.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:13.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:13.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:13.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:13.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:13.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:13.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:13.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:13.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:13.118][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[2025-04-17 04:30:13.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:13.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:13.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:13.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:13.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:13.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:13.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:13.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:13.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:13.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:13.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:13.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:13.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:13.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:13.138][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-devel_2025-02-19/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-04-17 04:30:13.140][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-04-17 04:30:13.143][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-17 04:30:13.145][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-04-17 04:30:13.146][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:13.148][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-17 04:30:13.149][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:13.150][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-17 04:30:13.152][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:13.153][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-04-17 04:30:13.155][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-17 04:30:13.156][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-17 04:30:13.158][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:13.159][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-04-17 04:30:13.161][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-17 04:30:13.162][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-04-17 04:30:13.162][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-04-17 04:30:13.162][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-04-17 04:30:13.162][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-04-17 04:30:13.162][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-04-17 04:30:13.162][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-04-17 04:30:13.162][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-04-17 04:30:13.162][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-04-17 04:30:13.162][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-04-17 04:30:13.162][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-04-17 04:30:13.162][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-04-17 04:30:13.164][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-17 04:30:13.165][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-17 04:30:13.165][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-17 04:30:13.165][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-17 04:30:13.167][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-17 04:30:13.168][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:30:13.170][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:30:13.171][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-17 04:30:13.172][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:30:13.174][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:30:13.175][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-17 04:30:13.177][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-17 04:30:13.177][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-04-17 04:30:13.178][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-17 04:30:13.179][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-17 04:30:13.181][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:13.182][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-04-17 04:30:13.182][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-04-17 04:30:13.184][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-17 04:30:13.187][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-17 04:30:13.189][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-04-17 04:30:13.191][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-17 04:30:13.193][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-17 04:30:13.196][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-17 04:30:13.201][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-04-17 04:30:13.203][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-04-17 04:30:13.205][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-04-17 04:30:13.207][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-04-17 04:30:13.209][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-17 04:30:13.211][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-17 04:30:13.213][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-04-17 04:30:13.214][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-04-17 04:30:13.216][biodb::testThat]
biodb.INFO [2025-04-17 04:30:13.218][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-04-17 04:30:13.219][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-17 04:30:13.221][biodb::testThat]
biodb.DEBUG[2025-04-17 04:30:13.225][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-04-17 04:30:13.231][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-17 04:30:13.233][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-04-17 04:30:13.235][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-17 04:30:13.237][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-04-17 04:30:13.242][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[2025-04-17 04:30:13.247][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:30:13.249][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:30:13.252][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-04-17 04:30:13.986][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-04-17 04:30:14.706][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:30:14.709][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2025-04-17 04:30:14.714][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2025-04-17 04:30:14.725][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-17 04:30:14.727][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-04-17 04:30:14.729][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-04-17 04:30:14.742][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-17 04:30:14.743][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:14.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:14.746][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:14.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:14.748][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:14.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-04-17 04:30:14.754][biodb::testContext]
biodb.INFO [2025-04-17 04:30:14.756][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-17 04:30:14.757][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-04-17 04:30:14.758][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-17 04:30:14.760][biodb::testContext]
biodb.INFO [2025-04-17 04:30:14.762][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-04-17 04:30:14.765][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-devel_2025-02-19/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-04-17 04:30:14.769][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-17 04:30:14.771][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-17 04:30:14.772][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-17 04:30:14.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:14.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:14.776][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[2025-04-17 04:30:14.778][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-17 04:30:14.779][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-17 04:30:14.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:14.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:14.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:14.784][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-17 04:30:14.786][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-17 04:30:14.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:14.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:14.789][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[2025-04-17 04:30:14.791][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-17 04:30:14.792][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-17 04:30:14.794][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-17 04:30:14.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:14.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:14.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:14.799][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-17 04:30:14.800][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-17 04:30:14.802][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-17 04:30:14.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:14.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:14.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:14.807][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-17 04:30:14.808][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-17 04:30:14.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:14.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:14.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:14.813][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-17 04:30:14.815][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-17 04:30:14.816][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-17 04:30:14.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:14.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:14.820][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[2025-04-17 04:30:14.821][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-17 04:30:14.823][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-17 04:30:14.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:14.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:14.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:14.828][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-17 04:30:14.829][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-17 04:30:14.830][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-17 04:30:14.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:14.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:14.834][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[2025-04-17 04:30:14.835][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-17 04:30:14.837][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-17 04:30:14.838][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-17 04:30:14.840][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-17 04:30:14.841][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-17 04:30:14.843][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-17 04:30:14.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:14.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:14.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:14.848][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-17 04:30:14.849][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-17 04:30:14.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:14.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:14.853][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[2025-04-17 04:30:14.854][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-17 04:30:14.855][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-17 04:30:14.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:14.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:14.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:14.860][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-17 04:30:14.862][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-17 04:30:14.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:14.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:14.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:14.867][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-17 04:30:14.868][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-17 04:30:14.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:14.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:14.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:14.873][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-17 04:30:14.875][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-17 04:30:14.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:14.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:14.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:14.880][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-17 04:30:14.881][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-17 04:30:14.886][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-17 04:30:14.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:14.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:14.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:14.891][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-17 04:30:14.893][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-17 04:30:14.894][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-17 04:30:14.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:14.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:14.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:14.899][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-17 04:30:14.902][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-17 04:30:14.903][self$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[2025-04-17 04:30:14.905][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:14.906][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-17 04:30:14.907][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:14.909][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-17 04:30:14.910][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-17 04:30:14.912][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-17 04:30:14.913][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-17 04:30:14.914][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-17 04:30:14.916][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:14.917][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-17 04:30:14.918][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-17 04:30:14.920][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:30:14.921][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:14.923][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-17 04:30:14.923][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-17 04:30:14.923][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-17 04:30:14.923][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-17 04:30:14.923][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-17 04:30:14.924][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-17 04:30:14.925][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:30:14.927][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:30:14.928][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-17 04:30:14.929][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:30:14.931][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:30:14.932][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-17 04:30:14.933][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:30:14.935][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-17 04:30:14.936][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-17 04:30:14.937][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-17 04:30:14.939][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:30:14.940][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-17 04:30:14.943][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-17 04:30:14.944][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-17 04:30:14.946][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:14.947][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-17 04:30:14.948][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:14.950][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-17 04:30:14.951][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-17 04:30:14.953][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-17 04:30:14.954][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-17 04:30:14.955][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-17 04:30:14.957][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:14.958][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-17 04:30:14.959][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-17 04:30:14.961][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:30:14.962][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:14.964][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-17 04:30:14.964][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-17 04:30:14.964][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-17 04:30:14.964][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-17 04:30:14.964][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-17 04:30:14.965][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-17 04:30:14.966][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:30:14.968][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:30:14.969][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-17 04:30:14.970][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:30:14.971][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:30:14.973][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-17 04:30:14.974][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:30:14.976][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-17 04:30:14.977][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-17 04:30:14.978][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-17 04:30:14.980][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:30:14.981][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-17 04:30:14.991][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:14.992][self$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[2025-04-17 04:30:14.994][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:14.995][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-17 04:30:14.996][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:14.998][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-17 04:30:14.999][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-17 04:30:15.001][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-17 04:30:15.002][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-17 04:30:15.003][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-17 04:30:15.005][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-17 04:30:15.006][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-17 04:30:15.007][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-17 04:30:15.009][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:30:15.010][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:15.011][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:30:15.013][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-17 04:30:15.014][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:30:15.016][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:30:15.017][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-17 04:30:15.018][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:30:15.020][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:30:15.021][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-17 04:30:15.022][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:30:15.024][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-17 04:30:15.025][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-17 04:30:15.027][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-17 04:30:15.028][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:30:15.030][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-17 04:30:15.032][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:15.034][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-17 04:30:15.035][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:15.036][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-17 04:30:15.038][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:15.039][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-17 04:30:15.040][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-17 04:30:15.042][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-17 04:30:15.043][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-17 04:30:15.045][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-17 04:30:15.046][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-17 04:30:15.047][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-17 04:30:15.049][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-17 04:30:15.050][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:30:15.052][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:15.053][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:30:15.055][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-17 04:30:15.056][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:30:15.057][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:30:15.058][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-17 04:30:15.060][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:30:15.061][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:30:15.062][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-17 04:30:15.064][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:30:15.065][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-17 04:30:15.066][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-17 04:30:15.068][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-17 04:30:15.069][self$setPropertyValue]
biodb.DEBUG[2025-04-17 04:30:15.071][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-17 04:30:15.072][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:15.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:15.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:15.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:15.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:15.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:15.079][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[2025-04-17 04:30:15.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:15.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:15.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:15.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:15.086][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.DEBUG[2025-04-17 04:30:15.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:15.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:15.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:15.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:15.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:15.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:15.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:15.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:15.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:15.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:15.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:15.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:15.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:15.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:15.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:15.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:15.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:15.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:15.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:15.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:15.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:15.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:15.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:15.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:15.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:15.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:15.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:15.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:15.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:15.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:15.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:15.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:15.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:15.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:15.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:15.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:15.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:15.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:15.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:15.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:15.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:15.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:15.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:15.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:15.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:15.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:15.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:15.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:15.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:15.147][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[2025-04-17 04:30:15.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:15.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:15.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:15.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:15.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:15.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:15.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:15.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:15.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:15.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:15.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:15.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:15.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:15.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:15.165][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[2025-04-17 04:30:15.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:15.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:15.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:15.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:15.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:15.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:15.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:15.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:15.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:15.178][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.DEBUG[2025-04-17 04:30:15.179][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-17 04:30:15.181][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-17 04:30:15.183][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-17 04:30:15.185][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-17 04:30:15.187][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-17 04:30:15.189][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-17 04:30:15.191][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-17 04:30:15.193][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-17 04:30:15.195][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-17 04:30:15.197][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-17 04:30:15.199][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-17 04:30:15.201][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-17 04:30:15.203][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-17 04:30:15.205][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-17 04:30:15.207][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-17 04:30:15.209][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-17 04:30:15.211][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-17 04:30:15.213][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-17 04:30:15.215][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-17 04:30:15.218][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-17 04:30:15.220][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-17 04:30:15.228][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-17 04:30:15.246][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-17 04:30:15.249][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-17 04:30:15.251][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-17 04:30:15.253][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-17 04:30:15.255][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-17 04:30:15.257][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-17 04:30:15.260][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-17 04:30:15.262][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-17 04:30:15.264][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-17 04:30:15.266][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-17 04:30:15.268][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-17 04:30:15.270][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-17 04:30:15.273][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-17 04:30:15.275][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-17 04:30:15.277][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-17 04:30:15.279][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-17 04:30:15.281][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-17 04:30:15.284][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-17 04:30:15.286][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-17 04:30:15.288][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-17 04:30:15.290][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-17 04:30:15.292][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-17 04:30:15.294][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-17 04:30:15.297][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-17 04:30:15.299][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-17 04:30:15.301][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-17 04:30:15.303][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-17 04:30:15.306][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-17 04:30:15.308][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-17 04:30:15.310][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-17 04:30:15.312][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-17 04:30:15.315][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-17 04:30:15.317][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-17 04:30:15.319][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-17 04:30:15.321][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-17 04:30:15.324][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-17 04:30:15.326][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-17 04:30:15.328][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-17 04:30:15.330][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-17 04:30:15.333][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-17 04:30:15.335][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-17 04:30:15.337][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-17 04:30:15.339][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-17 04:30:15.342][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-17 04:30:15.344][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-17 04:30:15.346][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-17 04:30:15.348][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-17 04:30:15.350][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-17 04:30:15.353][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-17 04:30:15.355][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-17 04:30:15.357][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-17 04:30:15.359][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-17 04:30:15.362][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-17 04:30:15.364][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-17 04:30:15.366][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-17 04:30:15.368][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-17 04:30:15.370][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-17 04:30:15.372][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-17 04:30:15.375][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-17 04:30:15.377][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-17 04:30:15.379][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-17 04:30:15.381][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-17 04:30:15.383][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-04-17 04:30:15.385][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-17 04:30:15.386][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:15.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:15.389][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:15.390][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.DEBUG[2025-04-17 04:30:15.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:15.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:15.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:15.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:15.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:15.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:15.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:15.402][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:15.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:15.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:15.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:15.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:15.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:15.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:15.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:15.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:15.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:15.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:15.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:15.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:15.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:15.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:15.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:15.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:15.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:15.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:15.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:15.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:15.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:15.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:15.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:15.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:15.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:15.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:15.439][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[2025-04-17 04:30:15.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:15.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:15.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:15.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:15.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:15.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:15.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:15.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:15.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:15.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:15.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:15.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:15.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:15.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:15.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:15.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:15.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:15.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:15.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:15.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:15.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:15.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:15.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:15.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:15.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:15.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:15.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:15.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:15.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:15.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:15.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:15.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:15.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:15.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:15.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:15.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:15.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:15.490][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:15.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:15.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:15.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:15.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:15.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:15.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:15.500][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:15.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:15.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:15.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:15.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:15.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:15.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:15.517][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:15.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:15.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:15.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:15.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:15.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:15.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:15.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:15.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:15.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:15.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:15.531][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[2025-04-17 04:30:15.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:15.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:15.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:15.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:15.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:15.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:15.541][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[2025-04-17 04:30:15.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:15.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:15.544][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:15.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:15.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:15.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:15.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:15.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-17 04:30:15.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:15.553][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:15.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:15.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:15.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:15.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:15.560][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-devel_2025-02-19/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-04-17 04:30:15.562][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-04-17 04:30:15.565][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-17 04:30:15.566][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-04-17 04:30:15.568][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:15.569][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-17 04:30:15.571][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:15.572][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-17 04:30:15.573][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:15.575][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-04-17 04:30:15.576][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-17 04:30:15.578][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-17 04:30:15.579][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:15.580][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-04-17 04:30:15.582][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-17 04:30:15.583][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-04-17 04:30:15.583][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-04-17 04:30:15.583][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-04-17 04:30:15.583][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-04-17 04:30:15.583][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-04-17 04:30:15.583][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-04-17 04:30:15.583][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-04-17 04:30:15.583][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-04-17 04:30:15.583][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-04-17 04:30:15.583][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-04-17 04:30:15.583][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-04-17 04:30:15.585][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-17 04:30:15.586][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-17 04:30:15.586][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-17 04:30:15.586][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-17 04:30:15.588][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-17 04:30:15.589][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:30:15.590][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:30:15.592][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-17 04:30:15.593][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-17 04:30:15.594][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-17 04:30:15.596][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-17 04:30:15.597][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-17 04:30:15.597][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-04-17 04:30:15.598][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-17 04:30:15.600][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-17 04:30:15.601][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-17 04:30:15.602][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-04-17 04:30:15.602][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-04-17 04:30:15.604][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-17 04:30:15.607][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-17 04:30:15.609][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-04-17 04:30:15.611][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-17 04:30:15.613][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-17 04:30:15.615][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-17 04:30:15.620][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-04-17 04:30:15.622][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-04-17 04:30:15.623][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-04-17 04:30:15.625][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-04-17 04:30:15.627][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-17 04:30:15.628][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-17 04:30:15.630][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-04-17 04:30:15.631][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-04-17 04:30:15.633][biodb::testThat]
biodb.INFO [2025-04-17 04:30:15.635][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-04-17 04:30:15.636][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-17 04:30:15.637][biodb::testThat]
biodb.DEBUG[2025-04-17 04:30:15.642][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-04-17 04:30:15.647][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-17 04:30:15.649][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-04-17 04:30:15.651][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-17 04:30:15.652][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-04-17 04:30:15.657][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-17 04:30:15.662][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-17 04:30:15.663][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-04-17 04:30:15.665][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-17 04:30:15.667][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2025-04-17 04:30:15.673][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-04-17 04:30:15.674][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-17 04:30:15.676][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2025-04-17 04:30:15.678][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-17 04:30:15.680][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-17 04:30:15.681][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-17 04:30:15.683][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-17 04:30:15.684][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-17 04:30:15.685][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-17 04:30:15.689][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:30:15.690][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:15.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:15.698][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:15.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:15.701][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:15.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-17 04:30:15.704][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2025-04-17 04:30:15.708][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-17 04:30:15.709][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-17 04:30:15.711][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2025-04-17 04:30:16.982][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2025-04-17 04:30:18.287][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-17 04:30:18.290][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2025-04-17 04:30:18.294][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2025-04-17 04:30:18.298][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2025-04-17 04:30:18.300][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-17 04:30:18.302][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-17 04:30:18.303][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-17 04:30:18.306][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-17 04:30:18.307][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:18.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:18.315][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:18.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:18.317][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:18.319][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.TRACE[2025-04-17 04:30:18.325][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:30:18.326][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:30:18.328][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:30:18.329][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:30:18.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:30:18.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:30:18.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:30:18.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:30:18.367][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:30:18.368][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:30:18.370][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:30:18.371][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:30:18.374][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-17 04:30:18.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-17 04:30:18.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:30:18.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:30:18.379][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:30:18.381][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:30:18.382][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:30:18.383][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:30:18.386][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-17 04:30:18.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-17 04:30:18.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:30:18.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:30:18.392][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-17 04:30:18.393][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-17 04:30:18.394][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:30:18.396][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:30:18.398][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-17 04:30:18.400][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-17 04:30:18.401][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:30:18.402][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:30:18.405][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:30:18.406][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:30:18.407][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:30:18.409][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:30:18.411][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:30:18.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-17 04:30:18.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:30:18.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:30:18.417][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:30:18.418][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:30:18.420][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:30:18.421][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:30:18.423][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-17 04:30:18.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-17 04:30:18.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:30:18.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:30:18.429][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:30:18.431][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:30:18.432][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:30:18.433][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:30:18.436][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:30:18.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-17 04:30:18.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:30:18.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:30:18.441][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:30:18.443][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:30:18.444][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:30:18.445][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:30:18.448][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-17 04:30:18.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-17 04:30:18.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:30:18.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:30:18.454][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:30:18.455][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:30:18.457][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:30:18.458][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:30:18.460][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-17 04:30:18.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-17 04:30:18.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:30:18.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:30:18.466][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:30:18.468][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:30:18.469][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:30:18.470][ef$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:30:18.473][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-17 04:30:18.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-17 04:30:18.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:30:18.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:30:18.478][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:30:18.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:30:18.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:30:18.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:30:18.484][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:30:18.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:30:18.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:30:18.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:30:18.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:30:18.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:30:18.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:30:18.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:30:18.495][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-17 04:30:18.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-17 04:30:18.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:30:18.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:30:18.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:30:18.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:30:18.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:30:18.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:30:18.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:30:18.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:30:18.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:30:18.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:30:18.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:30:18.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:30:18.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:30:18.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:30:18.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:30:18.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:30:18.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:30:18.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:30:18.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:30:18.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:30:18.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:30:18.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-17 04:30:18.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-17 04:30:18.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-17 04:30:18.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-17 04:30:18.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-17 04:30:18.536][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-04-17 04:30:18.541][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-17 04:30:18.543][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-04-17 04:30:18.544][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-04-17 04:30:18.545][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-17 04:30:18.547][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-17 04:30:18.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-17 04:30:18.549][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-17 04:30:18.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-17 04:30:18.552][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-17 04:30:18.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 386 ]
> 
> proc.time()
   user  system elapsed 
 25.508   1.852 118.231

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

nameusersystemelapsed
ChebiConn1.1770.0577.368
ChebiEntry0.2150.0060.221