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This page was generated on 2024-05-30 11:35:26 -0400 (Thu, 30 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4753
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4518
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 200/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbChebi 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-05-29 14:00:10 -0400 (Wed, 29 May 2024)
git_url: https://git.bioconductor.org/packages/biodbChebi
git_branch: RELEASE_3_19
git_last_commit: fad38a4
git_last_commit_date: 2024-04-30 11:37:31 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for biodbChebi on lconway


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

raw results

Summary

Package: biodbChebi
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.10.0.tar.gz
StartedAt: 2024-05-29 19:20:37 -0400 (Wed, 29 May 2024)
EndedAt: 2024-05-29 19:23:29 -0400 (Wed, 29 May 2024)
EllapsedTime: 171.9 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbChebi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/biodbChebi.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.10.0’
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biodbChebi
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘biodbChebi’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbChebi)

Tests output

biodbChebi.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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

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

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

> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2024-05-29 19:21:38.082][biodb::testContext]
biodb.INFO [2024-05-29 19:21:38.087][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-29 19:21:38.088][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-05-29 19:21:38.089][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-29 19:21:38.091][biodb::testContext]
biodb.INFO [2024-05-29 19:21:38.100][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-29 19:21:38.104][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-29 19:21:38.115][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-29 19:21:38.117][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-29 19:21:38.118][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-29 19:21:38.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.124][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-29 19:21:38.153][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-29 19:21:38.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.158][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-29 19:21:38.159][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-29 19:21:38.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.165][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-29 19:21:38.166][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-29 19:21:38.167][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-29 19:21:38.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.172][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-29 19:21:38.188][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-29 19:21:38.190][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-29 19:21:38.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.196][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-29 19:21:38.197][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-29 19:21:38.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.200][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[2024-05-29 19:21:38.202][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-29 19:21:38.203][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-29 19:21:38.204][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-29 19:21:38.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.209][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-29 19:21:38.211][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-29 19:21:38.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.213][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[2024-05-29 19:21:38.214][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-29 19:21:38.216][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-29 19:21:38.217][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-29 19:21:38.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.222][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-29 19:21:38.223][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-29 19:21:38.224][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-29 19:21:38.226][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-29 19:21:38.227][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-29 19:21:38.229][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-29 19:21:38.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.231][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[2024-05-29 19:21:38.233][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-29 19:21:38.234][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-29 19:21:38.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.239][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-29 19:21:38.240][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-29 19:21:38.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.245][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-29 19:21:38.246][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-29 19:21:38.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.251][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-29 19:21:38.252][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-29 19:21:38.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.257][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-29 19:21:38.259][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-29 19:21:38.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.264][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-29 19:21:38.265][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-29 19:21:38.294][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-29 19:21:38.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.300][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-29 19:21:38.301][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-29 19:21:38.303][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-29 19:21:38.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.310][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-29 19:21:38.355][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-29 19:21:38.377][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-29 19:21:38.379][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-29 19:21:38.380][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-29 19:21:38.382][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-29 19:21:38.383][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-29 19:21:38.385][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-29 19:21:38.386][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-29 19:21:38.388][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-29 19:21:38.389][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-29 19:21:38.390][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-29 19:21:38.392][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-29 19:21:38.393][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-29 19:21:38.394][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:21:38.395][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-29 19:21:38.397][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-29 19:21:38.397][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-29 19:21:38.397][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-29 19:21:38.397][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-29 19:21:38.397][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-29 19:21:38.398][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-29 19:21:38.399][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:21:38.400][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:21:38.400][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-29 19:21:38.402][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:21:38.403][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:21:38.404][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-29 19:21:38.406][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:21:38.407][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-29 19:21:38.408][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-29 19:21:38.409][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-29 19:21:38.410][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:21:38.412][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-29 19:21:38.414][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-29 19:21:38.416][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-29 19:21:38.417][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-29 19:21:38.418][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-29 19:21:38.419][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-29 19:21:38.421][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-29 19:21:38.422][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-29 19:21:38.423][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-29 19:21:38.424][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-29 19:21:38.425][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-29 19:21:38.426][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-29 19:21:38.427][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-29 19:21:38.428][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-29 19:21:38.429][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:21:38.430][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-29 19:21:38.431][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-29 19:21:38.431][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-29 19:21:38.431][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-29 19:21:38.431][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-29 19:21:38.431][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-29 19:21:38.432][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-29 19:21:38.434][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:21:38.435][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:21:38.436][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-29 19:21:38.438][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:21:38.439][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:21:38.440][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-29 19:21:38.441][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:21:38.443][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-29 19:21:38.444][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-29 19:21:38.446][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-29 19:21:38.447][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:21:38.449][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-29 19:21:38.451][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-29 19:21:38.452][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-29 19:21:38.453][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-29 19:21:38.454][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-29 19:21:38.455][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-29 19:21:38.456][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-29 19:21:38.458][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-29 19:21:38.459][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-29 19:21:38.460][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-29 19:21:38.461][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-29 19:21:38.462][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-29 19:21:38.464][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-29 19:21:38.465][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-29 19:21:38.467][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:21:38.468][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-29 19:21:38.477][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:21:38.478][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-29 19:21:38.479][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:21:38.481][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:21:38.482][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-29 19:21:38.483][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:21:38.484][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:21:38.484][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-29 19:21:38.486][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:21:38.487][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-29 19:21:38.488][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-29 19:21:38.490][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-29 19:21:38.491][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:21:38.492][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-29 19:21:38.495][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-29 19:21:38.496][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-29 19:21:38.497][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-29 19:21:38.499][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-29 19:21:38.500][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-29 19:21:38.501][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-29 19:21:38.502][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-29 19:21:38.503][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-29 19:21:38.504][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-29 19:21:38.505][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-29 19:21:38.507][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-29 19:21:38.508][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-29 19:21:38.509][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-29 19:21:38.510][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:21:38.511][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-29 19:21:38.513][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:21:38.514][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-29 19:21:38.515][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:21:38.516][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:21:38.517][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-29 19:21:38.518][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:21:38.519][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:21:38.520][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-29 19:21:38.522][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:21:38.523][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-29 19:21:38.525][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-29 19:21:38.526][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-29 19:21:38.528][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:21:38.533][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-29 19:21:38.534][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.535][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.DEBUG[2024-05-29 19:21:38.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:38.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:38.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:38.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:38.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:38.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:38.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.551][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[2024-05-29 19:21:38.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:38.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:38.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:38.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:38.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:38.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:38.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:38.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:38.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.572][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.DEBUG[2024-05-29 19:21:38.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:38.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:38.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.578][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.DEBUG[2024-05-29 19:21:38.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:38.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:38.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.582][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[2024-05-29 19:21:38.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:38.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:38.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:38.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:38.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:38.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:38.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:38.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:38.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:38.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:38.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.610][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.DEBUG[2024-05-29 19:21:38.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:38.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:38.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:38.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:38.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.620][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[2024-05-29 19:21:38.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:38.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:38.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.627][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-29 19:21:38.633][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-29 19:21:38.635][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-29 19:21:38.636][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-29 19:21:38.638][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-29 19:21:38.640][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-29 19:21:38.642][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-29 19:21:38.644][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-29 19:21:38.645][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-29 19:21:38.647][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-29 19:21:38.649][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-29 19:21:38.651][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-29 19:21:38.653][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-29 19:21:38.655][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-29 19:21:38.657][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-29 19:21:38.659][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-29 19:21:38.660][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-29 19:21:38.662][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-29 19:21:38.664][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-29 19:21:38.666][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-29 19:21:38.667][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-29 19:21:38.670][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-29 19:21:38.672][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-29 19:21:38.673][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-29 19:21:38.675][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-29 19:21:38.677][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-29 19:21:38.679][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-29 19:21:38.681][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-29 19:21:38.683][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-29 19:21:38.685][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-29 19:21:38.687][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-29 19:21:38.688][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-29 19:21:38.690][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-29 19:21:38.692][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-29 19:21:38.694][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-29 19:21:38.695][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-29 19:21:38.697][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-29 19:21:38.699][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-29 19:21:38.702][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-29 19:21:38.704][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-29 19:21:38.707][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-29 19:21:38.709][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-29 19:21:38.712][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-29 19:21:38.714][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-29 19:21:38.716][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-29 19:21:38.718][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-29 19:21:38.720][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-29 19:21:38.722][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-29 19:21:38.724][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-29 19:21:38.732][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-29 19:21:38.734][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-29 19:21:38.736][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-29 19:21:38.738][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-29 19:21:38.740][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-29 19:21:38.741][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-29 19:21:38.743][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-29 19:21:38.745][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-29 19:21:38.747][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-29 19:21:38.748][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-29 19:21:38.750][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-29 19:21:38.752][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-29 19:21:38.753][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-29 19:21:38.755][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-29 19:21:38.757][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-29 19:21:38.759][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-29 19:21:38.761][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-29 19:21:38.762][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-29 19:21:38.764][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-29 19:21:38.766][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-29 19:21:38.768][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-29 19:21:38.770][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-29 19:21:38.771][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-29 19:21:38.773][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-29 19:21:38.775][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-29 19:21:38.777][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-29 19:21:38.778][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-29 19:21:38.779][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-29 19:21:38.781][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-29 19:21:38.783][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-29 19:21:38.785][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-29 19:21:38.787][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-29 19:21:38.788][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-29 19:21:38.790][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-29 19:21:38.797][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-29 19:21:38.800][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-29 19:21:38.804][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-29 19:21:38.805][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:38.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:38.807][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:38.817][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:38.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:38.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:38.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:38.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:38.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:38.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:38.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:38.833][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:38.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:38.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:38.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:38.842][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:38.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:38.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:38.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.846][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[2024-05-29 19:21:38.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:38.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:38.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:38.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:38.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:38.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:38.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:38.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:38.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.862][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[2024-05-29 19:21:38.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:38.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:38.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:38.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:38.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:38.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:38.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:38.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:38.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:38.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:38.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:38.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:38.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:38.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:38.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:38.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:38.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:38.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:38.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:38.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:38.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:38.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:38.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:38.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:38.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:38.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:38.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:38.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:38.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:38.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:38.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:38.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:38.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:38.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:38.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:38.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:38.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:38.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:38.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:38.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:38.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:21:38.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:38.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:38.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:38.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:38.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:38.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:38.951][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-05-29 19:21:38.963][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-05-29 19:21:38.966][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-29 19:21:38.967][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-29 19:21:38.969][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-29 19:21:38.970][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-29 19:21:38.971][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-29 19:21:38.980][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-29 19:21:38.981][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-29 19:21:38.983][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-05-29 19:21:38.984][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-29 19:21:38.985][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-29 19:21:38.986][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-29 19:21:38.988][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-05-29 19:21:38.989][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-29 19:21:38.990][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-05-29 19:21:38.990][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-05-29 19:21:38.990][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-05-29 19:21:38.990][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-05-29 19:21:38.990][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-05-29 19:21:38.990][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-05-29 19:21:38.990][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-05-29 19:21:38.990][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-05-29 19:21:38.990][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-05-29 19:21:38.990][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-05-29 19:21:38.990][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-05-29 19:21:38.992][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-29 19:21:39.017][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-29 19:21:39.017][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-29 19:21:39.017][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-29 19:21:39.019][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-29 19:21:39.020][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:21:39.022][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:21:39.023][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-29 19:21:39.025][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:21:39.026][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:21:39.027][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-29 19:21:39.028][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-29 19:21:39.028][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-05-29 19:21:39.029][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-29 19:21:39.029][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-29 19:21:39.030][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-29 19:21:39.032][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-05-29 19:21:39.032][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-05-29 19:21:39.040][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-29 19:21:39.043][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-29 19:21:39.045][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-05-29 19:21:39.047][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-29 19:21:39.049][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-29 19:21:39.051][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-29 19:21:39.083][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-05-29 19:21:39.085][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-05-29 19:21:39.091][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-05-29 19:21:39.097][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-05-29 19:21:39.103][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-29 19:21:39.105][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-29 19:21:39.107][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-05-29 19:21:39.109][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-05-29 19:21:39.121][biodb::testThat]
biodb.INFO [2024-05-29 19:21:39.123][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-05-29 19:21:39.124][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:21:39.126][biodb::testThat]
biodb.TRACE[2024-05-29 19:21:39.152][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2024-05-29 19:21:39.154][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-29 19:21:39.159][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-29 19:21:39.169][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:39.171][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:39.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:39.193][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:39.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:39.196][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:39.198][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.TRACE[2024-05-29 19:21:39.210][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:39.212][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:39.213][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.214][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:39.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:39.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.240][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:21:39.241][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:21:39.242][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.243][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.279][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:21:39.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:21:39.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.285][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:21:39.287][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:21:39.288][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.289][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.291][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:21:39.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:21:39.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.296][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:21:39.298][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:21:39.299][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.300][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.302][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:21:39.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:21:39.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.307][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:21:39.308][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:21:39.309][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.310][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.324][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:21:39.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:21:39.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.330][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:39.332][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:39.333][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.335][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.336][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:39.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:39.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.342][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:21:39.343][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:39.345][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.346][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.347][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:21:39.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:39.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.353][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:39.354][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:39.356][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.357][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.359][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:39.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:39.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.363][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:39.364][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:39.365][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.367][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.369][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:39.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:39.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.374][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:21:39.375][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:21:39.376][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.377][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.379][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:21:39.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:21:39.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.385][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:21:39.387][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:21:39.388][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.389][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.391][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:21:39.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:21:39.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.396][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:39.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:39.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.401][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:39.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:39.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:39.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:39.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.410][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:39.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:39.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:39.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:39.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:39.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:39.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:39.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:39.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:39.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:39.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:39.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:39.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.483][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:39.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:39.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:21:39.487][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-05-29 19:21:39.491][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:21:39.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:21:39.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.496][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:21:39.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:21:39.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.568][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:21:39.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:21:39.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.573][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:21:39.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:21:39.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.578][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:39.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:39.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.583][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:39.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:39.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.588][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-29 19:21:39.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-29 19:21:39.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.592][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-29 19:21:39.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-29 19:21:39.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.596][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-29 19:21:39.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-29 19:21:39.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.602][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-29 19:21:39.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-29 19:21:39.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:39.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:39.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.653][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:39.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:39.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:39.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:39.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:39.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:39.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:39.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:39.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.684][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:39.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:39.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:39.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:39.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:39.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:39.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.697][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:39.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:39.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.701][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:39.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:39.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.707][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:39.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:39.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:39.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:39.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:39.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:39.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:39.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:39.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.763][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:39.765][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:39.766][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.768][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:39.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:39.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.787][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:39.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:39.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.793][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:39.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:39.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.805][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:39.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:39.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.811][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:39.813][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:39.814][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.815][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.816][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:39.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:39.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.834][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:39.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:39.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.840][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:39.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:39.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.845][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:39.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:39.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.852][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:39.853][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:39.854][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.855][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.857][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:39.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:39.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.874][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:21:39.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:21:39.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.880][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:21:39.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:21:39.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.885][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:21:39.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:21:39.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.890][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:21:39.892][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:21:39.893][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.894][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.895][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:21:39.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:21:39.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.912][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:39.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:39.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.918][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:39.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:39.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.923][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:39.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:39.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.927][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:39.929][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:39.931][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.932][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.933][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:39.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:39.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.952][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:39.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:39.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.960][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:39.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:39.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.964][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:39.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:39.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.970][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:39.972][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:39.973][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.974][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.975][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:39.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:39.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.993][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:21:39.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:21:39.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:39.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:39.999][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:21:40.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:21:40.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.003][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:21:40.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:21:40.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.009][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:21:40.010][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:21:40.011][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.013][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.014][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:21:40.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:21:40.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.034][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-29 19:21:40.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:21:40.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.045][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-29 19:21:40.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:21:40.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.050][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-29 19:21:40.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:21:40.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.055][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-29 19:21:40.056][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:21:40.057][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.058][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.059][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-29 19:21:40.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:21:40.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.075][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:40.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:40.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.079][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:40.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:40.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.084][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:40.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:40.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.088][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:40.089][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:40.090][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.091][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.092][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:40.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:40.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.111][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:21:40.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:21:40.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.115][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:21:40.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:21:40.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.120][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:21:40.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:21:40.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.126][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:21:40.127][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:21:40.128][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.130][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.132][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:21:40.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:21:40.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.149][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:21:40.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:21:40.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.155][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:21:40.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:21:40.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.161][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:21:40.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:21:40.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.165][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:21:40.167][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:21:40.168][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.169][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.171][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:21:40.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:21:40.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.189][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:21:40.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:21:40.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.195][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:21:40.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:21:40.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.200][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:21:40.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:21:40.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.206][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:21:40.207][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:21:40.208][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.210][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.211][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:21:40.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:21:40.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.230][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:40.231][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:40.233][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.234][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.243][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:21:40.244][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:21:40.245][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.246][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.254][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:21:40.255][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:21:40.256][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.257][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.263][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:21:40.264][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:21:40.265][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.266][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.289][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:21:40.291][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:21:40.293][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.294][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.306][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:40.308][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:40.309][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.311][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.317][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:40.318][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:40.320][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.321][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.328][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:40.330][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:40.331][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.332][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.340][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-29 19:21:40.341][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:21:40.342][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.343][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.350][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:40.351][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:40.353][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.354][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.362][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:21:40.364][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:21:40.365][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.366][ef$get] fields variable is a list.
biodb.INFO [2024-05-29 19:21:40.380][biodb::testThat]
biodb.INFO [2024-05-29 19:21:40.382][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-05-29 19:21:40.384][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:21:40.385][biodb::testThat]
biodb.DEBUG[2024-05-29 19:21:40.406][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-05-29 19:21:40.416][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-29 19:21:40.421][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-05-29 19:21:40.423][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-29 19:21:40.425][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-05-29 19:21:40.427][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-29 19:21:40.450][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-29 19:21:40.452][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-29 19:21:40.454][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:40.455][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:40.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:40.466][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:40.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:40.469][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:40.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:21:40.475][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:40.476][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:40.478][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.479][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.481][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:40.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:40.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.516][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:21:40.518][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:21:40.519][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.520][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.522][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:21:40.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:21:40.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.528][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:21:40.531][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:21:40.535][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.537][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.538][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:21:40.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:21:40.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.545][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:21:40.547][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:21:40.548][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.549][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.550][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:21:40.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:21:40.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.554][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:21:40.555][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:21:40.557][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.558][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.559][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:21:40.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:21:40.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.563][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:40.565][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:40.566][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.567][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.568][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:40.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:40.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.575][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:21:40.576][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:40.577][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.578][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.580][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:21:40.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:40.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.584][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:40.585][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:40.586][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.587][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.589][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:40.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:40.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.594][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:40.595][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:40.597][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.598][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.600][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:40.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:40.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.604][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:21:40.605][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:21:40.607][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.607][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.609][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:21:40.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:21:40.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.614][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:21:40.615][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:21:40.617][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.618][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.620][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:21:40.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:21:40.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.625][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:40.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:40.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.631][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:40.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:40.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:40.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:40.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.640][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:40.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:40.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:40.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:40.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:40.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:40.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.653][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:40.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:40.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:40.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:40.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:40.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:40.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:40.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:40.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:21:40.673][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-05-29 19:21:40.674][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-05-29 19:21:40.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-05-29 19:21:40.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.679][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-05-29 19:21:40.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-05-29 19:21:40.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.682][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-05-29 19:21:40.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-05-29 19:21:40.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-29 19:21:40.702][biodb::testThat]
biodb.INFO [2024-05-29 19:21:40.703][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-05-29 19:21:40.704][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:21:40.705][biodb::testThat]
biodb.TRACE[2024-05-29 19:21:40.709][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:40.711][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:40.712][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.714][ef$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:21:40.715][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-05-29 19:21:40.760][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:40.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:40.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.765][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:40.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:40.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:40.769][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:40.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:40.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:40.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:21:40.779][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-05-29 19:21:40.786][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-05-29 19:21:40.815][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-29 19:21:40.835][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-05-29 19:21:40.837][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-29 19:21:40.839][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-05-29 19:21:40.872][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-29 19:21:40.877][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:21:40.879][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:21:40.881][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-05-29 19:21:41.545][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-05-29 19:21:42.072][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:21:42.076][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-05-29 19:21:42.095][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-05-29 19:21:42.099][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-05-29 19:21:42.118][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:42.120][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:42.121][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:42.122][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:42.124][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:42.125][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:42.127][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:42.128][ef$get] fields variable is a list.
biodb.INFO [2024-05-29 19:21:42.136][biodb::testThat]
biodb.INFO [2024-05-29 19:21:42.137][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-05-29 19:21:42.139][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:21:42.140][biodb::testThat]
biodb.TRACE[2024-05-29 19:21:42.187][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:42.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:42.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:42.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:42.193][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:42.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:42.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:42.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:42.198][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:42.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:42.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:42.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:21:42.280][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-29 19:21:42.284][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-29 19:21:42.286][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-29 19:21:42.288][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-29 19:21:42.290][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-05-29 19:21:42.317][biodb::testThat]
biodb.INFO [2024-05-29 19:21:42.318][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-05-29 19:21:42.320][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:21:42.322][biodb::testThat]
biodb.TRACE[2024-05-29 19:21:42.359][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:21:42.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:21:42.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:42.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:42.364][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:21:42.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:21:42.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:42.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:42.369][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:21:42.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:21:42.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:42.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:42.375][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:21:42.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:21:42.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:42.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:42.379][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:42.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:42.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:42.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:42.385][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:42.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:42.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:42.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:42.390][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-29 19:21:42.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-29 19:21:42.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:42.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:42.395][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-29 19:21:42.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-29 19:21:42.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:42.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:42.401][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-29 19:21:42.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-29 19:21:42.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:42.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:42.406][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-29 19:21:42.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-29 19:21:42.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:42.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:42.435][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:21:42.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:21:42.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:42.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:42.440][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:21:42.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:21:42.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:42.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:42.445][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:21:42.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:21:42.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:42.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:42.450][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:21:42.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:21:42.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:42.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:42.455][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:42.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:42.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:42.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:42.460][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:42.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:42.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:42.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:42.464][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-29 19:21:42.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-29 19:21:42.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:42.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:42.470][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-29 19:21:42.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-29 19:21:42.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:42.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:42.475][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-29 19:21:42.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-29 19:21:42.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:42.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:42.479][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-29 19:21:42.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-29 19:21:42.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:42.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-29 19:21:42.501][biodb::testThat]
biodb.INFO [2024-05-29 19:21:42.502][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-05-29 19:21:42.504][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:21:42.505][biodb::testThat]
biodb.INFO [2024-05-29 19:21:42.517][biodb::testThat]
biodb.INFO [2024-05-29 19:21:42.518][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-05-29 19:21:42.519][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:21:42.520][biodb::testThat]
biodb.INFO [2024-05-29 19:21:42.532][biodb::testThat]
biodb.INFO [2024-05-29 19:21:42.533][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-05-29 19:21:42.535][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:21:42.536][biodb::testThat]
biodb.DEBUG[2024-05-29 19:21:42.542][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-05-29 19:21:43.271][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-05-29 19:21:44.313][biodb::testThat]
biodb.INFO [2024-05-29 19:21:44.314][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-05-29 19:21:44.316][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:21:44.317][biodb::testThat]
biodb.DEBUG[2024-05-29 19:21:44.725][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=15440&dimensions=400.
biodb.TRACE[2024-05-29 19:21:45.100][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:45.102][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:45.103][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:45.105][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:45.106][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:45.107][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:45.109][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:45.110][ef$get] fields variable is a list.
biodb.INFO [2024-05-29 19:21:45.112][biodb::testThat]
biodb.INFO [2024-05-29 19:21:45.114][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-05-29 19:21:45.115][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:21:45.116][biodb::testThat]
biodb.TRACE[2024-05-29 19:21:45.133][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:45.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:45.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:45.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:45.137][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:45.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:45.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:45.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:45.142][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:45.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:45.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:45.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:21:45.271][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-29 19:21:45.275][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-29 19:21:45.277][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-29 19:21:45.278][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-29 19:21:45.280][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-05-29 19:21:45.361][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-29 19:21:45.366][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-29 19:21:45.368][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-29 19:21:45.369][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-29 19:21:45.370][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-05-29 19:21:45.390][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-29 19:21:45.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-29 19:21:45.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:45.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:45.402][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:45.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:45.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:45.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:45.408][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:45.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:45.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:45.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:45.413][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:45.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:45.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:45.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:45.419][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:45.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:45.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:45.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:45.424][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:45.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:45.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:45.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:21:45.436][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-29 19:21:45.456][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:21:45.458][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:21:45.481][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-05-29 19:21:45.819][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-05-29 19:21:46.154][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:21:46.156][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-05-29 19:21:46.179][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-05-29 19:21:46.194][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:46.196][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:46.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:46.204][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:46.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:46.216][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:46.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:46.219][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-05-29 19:21:46.276][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-29 19:21:46.278][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-05-29 19:21:46.280][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-29 19:21:46.282][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-29 19:21:46.283][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-29 19:21:46.285][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-29 19:21:46.286][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-29 19:21:46.287][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-29 19:21:46.290][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:46.291][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:46.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:46.299][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:46.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:46.303][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:46.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:46.306][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-05-29 19:21:46.310][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:21:46.311][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:21:46.312][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-05-29 19:21:46.651][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-05-29 19:21:46.996][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:21:46.999][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-05-29 19:21:47.004][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-05-29 19:21:47.008][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-05-29 19:21:47.011][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-29 19:21:47.014][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-29 19:21:47.016][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-29 19:21:47.018][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:47.019][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:47.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:47.028][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:47.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:47.042][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:47.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:21:47.046][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:47.047][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:47.048][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:47.049][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:47.050][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:47.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:47.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:47.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:47.056][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:21:47.057][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:21:47.058][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:47.059][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:47.061][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:21:47.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:21:47.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:47.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:47.066][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:21:47.067][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:21:47.068][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:47.069][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:47.070][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:21:47.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:21:47.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:47.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:47.076][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:21:47.077][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:21:47.078][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:47.079][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:47.081][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:21:47.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:21:47.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:47.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:47.085][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:21:47.086][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:21:47.087][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:47.089][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:47.091][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:21:47.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:21:47.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:47.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:47.096][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:47.097][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:47.099][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:47.100][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:47.101][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:21:47.103][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:47.104][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:47.105][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:47.106][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:21:47.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:47.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:47.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:47.111][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:47.112][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:47.113][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:47.114][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:47.116][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:47.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:47.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:47.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:47.121][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:47.122][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:47.123][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:47.124][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:47.126][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:47.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:47.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:47.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:47.132][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:21:47.133][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:21:47.134][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:47.135][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:47.137][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:21:47.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:21:47.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:47.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:47.142][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:21:47.143][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:21:47.145][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:47.146][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:47.147][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:21:47.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:21:47.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:47.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:47.151][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:47.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:47.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:47.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:47.155][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:47.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:47.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:47.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:47.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:47.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:47.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:47.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:47.162][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:47.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:47.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:47.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:47.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:47.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:47.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:47.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:47.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:47.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:47.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:47.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:47.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:47.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:47.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:47.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:47.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:47.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:47.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:47.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:47.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:47.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:47.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:47.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:47.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:47.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:47.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:47.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:21:47.199][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-05-29 19:21:47.214][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:47.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:47.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:47.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:47.222][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:47.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:47.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:47.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:47.227][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:47.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:47.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:47.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:21:47.231][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-29 19:21:47.234][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:21:47.235][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:21:47.238][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-05-29 19:21:47.577][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-05-29 19:21:47.914][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:21:47.917][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-05-29 19:21:47.922][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-05-29 19:21:47.944][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:47.946][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:47.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:47.955][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:47.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:47.957][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:47.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:21:47.959][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:47.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:47.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:47.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:47.964][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:47.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:47.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:47.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:47.969][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:47.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:47.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:47.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:21:47.973][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:47.974][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:47.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:47.982][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:47.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:47.985][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:47.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:47.987][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-05-29 19:21:47.995][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-29 19:21:48.002][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-05-29 19:21:48.005][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-29 19:21:48.007][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-29 19:21:48.008][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-29 19:21:48.010][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-29 19:21:48.011][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-29 19:21:48.012][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-29 19:21:48.027][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:48.037][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:48.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:48.051][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:48.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:48.060][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:48.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:48.067][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-05-29 19:21:48.071][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:21:48.072][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:21:48.074][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-05-29 19:21:48.436][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-05-29 19:21:48.772][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:21:48.775][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-05-29 19:21:48.780][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-05-29 19:21:48.784][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-05-29 19:21:48.786][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-29 19:21:48.787][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-29 19:21:48.788][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-29 19:21:48.790][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:48.791][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:48.792][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:48.800][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:48.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:48.803][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:48.804][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.TRACE[2024-05-29 19:21:48.807][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:48.809][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:48.810][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:48.811][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:48.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:48.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:48.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:48.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:48.838][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:21:48.839][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:21:48.841][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:48.842][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:48.844][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:21:48.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:21:48.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:48.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:48.849][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:21:48.850][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:21:48.852][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:48.855][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:48.860][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:21:48.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:21:48.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:48.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:48.866][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:21:48.867][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:21:48.869][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:48.870][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:48.871][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:21:48.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:21:48.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:48.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:48.876][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:21:48.877][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:21:48.878][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:48.879][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:48.880][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:21:48.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:21:48.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:48.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:48.885][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:48.886][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:48.887][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:48.888][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:48.898][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:21:48.900][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:48.901][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:48.903][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:48.904][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:21:48.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:48.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:48.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:48.910][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:48.911][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:48.912][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:48.914][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:48.915][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:48.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:48.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:48.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:48.920][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:48.921][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:48.923][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:48.924][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:48.926][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:48.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:48.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:48.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:48.931][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:21:48.933][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:21:48.934][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:48.936][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:48.938][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:21:48.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:21:48.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:48.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:48.943][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:21:48.944][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:21:48.945][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:48.946][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:48.947][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:21:48.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:21:48.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:48.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:48.953][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:48.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:48.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:48.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:48.956][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:48.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:48.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:48.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:48.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:48.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:48.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:48.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:48.964][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:48.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:48.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:48.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:48.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:48.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:48.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:48.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:48.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:48.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:48.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:48.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:48.979][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:48.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:48.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:48.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:48.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:48.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:48.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:48.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:48.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:48.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:48.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:48.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:48.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:48.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:48.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:48.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:21:48.996][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-05-29 19:21:48.997][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:48.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:49.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:49.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:49.002][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:49.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:49.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:49.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:49.008][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:49.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:49.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:49.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:21:49.050][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-29 19:21:49.054][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-29 19:21:49.056][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-29 19:21:49.058][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-29 19:21:49.060][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-05-29 19:21:49.063][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:49.065][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:49.066][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:49.073][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:49.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:49.076][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:49.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:21:49.079][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:49.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:49.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:49.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:49.083][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:49.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:49.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:49.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:49.089][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:49.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:49.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:49.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:21:49.094][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:49.095][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:49.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:49.104][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:49.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:49.107][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:49.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:49.110][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-05-29 19:21:49.111][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-29 19:21:49.114][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-05-29 19:21:49.115][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-29 19:21:49.117][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-29 19:21:49.119][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-29 19:21:49.120][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-29 19:21:49.122][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-29 19:21:49.123][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-29 19:21:49.126][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:49.127][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:49.128][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:49.135][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:49.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:49.137][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:49.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:49.139][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-05-29 19:21:49.142][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:21:49.143][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:21:49.145][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-05-29 19:21:49.486][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-05-29 19:21:49.826][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:21:49.829][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-05-29 19:21:49.835][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-05-29 19:21:49.839][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-05-29 19:21:49.841][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-29 19:21:49.843][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-29 19:21:49.844][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-29 19:21:49.847][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:49.848][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:49.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:49.856][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:49.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:49.859][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:49.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:21:49.862][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:49.864][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:49.865][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:49.867][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:49.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:49.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:49.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:49.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:49.874][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:21:49.876][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:21:49.877][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:49.878][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:49.880][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:21:49.881][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:21:49.882][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:49.883][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:49.884][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:21:49.896][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:21:49.898][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:49.899][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:49.901][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:21:49.902][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:21:49.903][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:49.904][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:49.906][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:49.908][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:49.909][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:49.910][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:49.912][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:21:49.914][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:49.915][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:49.916][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:49.917][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:49.919][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:49.920][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:49.921][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:49.923][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:49.925][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:49.926][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:49.927][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:49.929][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:49.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:49.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:49.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:49.933][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:21:49.934][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:21:49.935][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:49.936][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:49.938][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:21:49.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:21:49.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:49.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:49.943][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:21:49.944][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:21:49.946][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:49.947][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:49.949][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:49.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:49.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:49.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:49.953][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:49.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:49.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:49.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:49.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:49.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:49.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:49.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:49.963][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:49.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:49.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:49.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:49.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:49.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:49.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:49.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:49.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:49.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:49.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:49.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:49.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:49.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:49.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:49.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:49.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:49.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:49.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:49.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:49.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:49.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:49.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:49.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:49.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:49.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:49.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:50.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:21:50.001][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-05-29 19:21:50.003][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:50.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:50.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:50.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:50.008][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:50.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:50.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:50.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:50.013][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:50.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:50.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:50.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:50.019][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:50.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:50.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:50.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:50.025][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:50.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:50.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:50.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:21:50.031][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:50.032][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:50.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:50.042][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:50.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:50.054][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:50.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:50.057][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-05-29 19:21:50.058][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-29 19:21:50.060][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-05-29 19:21:50.062][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-29 19:21:50.064][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-29 19:21:50.065][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-29 19:21:50.067][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-29 19:21:50.068][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-29 19:21:50.069][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-29 19:21:50.072][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:50.073][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:50.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:50.082][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:50.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:50.085][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:50.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:50.088][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-05-29 19:21:50.090][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:21:50.092][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:21:50.093][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-05-29 19:21:50.447][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-05-29 19:21:50.791][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:21:50.804][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-05-29 19:21:50.810][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-05-29 19:21:50.813][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-05-29 19:21:50.815][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-29 19:21:50.817][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-29 19:21:50.820][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-29 19:21:50.825][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:50.829][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:50.830][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:50.838][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:50.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:50.840][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:50.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:21:50.846][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:50.847][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:50.848][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:50.849][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:50.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:50.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:50.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:50.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:50.855][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:21:50.856][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:21:50.858][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:50.859][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:50.861][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:21:50.862][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:21:50.864][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:50.865][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:50.867][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:21:50.868][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:21:50.869][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:50.869][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:50.871][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:21:50.873][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:21:50.874][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:50.874][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:50.876][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:50.877][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:50.877][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:50.879][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:50.880][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:21:50.881][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:50.882][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:50.883][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:50.884][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:50.885][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:50.886][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:50.887][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:50.889][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:50.890][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:50.892][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:50.893][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:50.895][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:50.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:50.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:50.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:50.901][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:21:50.902][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:21:50.903][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:50.904][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:50.906][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:21:50.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:21:50.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:50.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:50.912][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:21:50.920][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:21:50.926][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:50.927][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:50.929][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:50.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:50.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:50.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:50.934][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:50.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:50.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:50.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:50.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:50.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:50.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:50.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:50.945][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:50.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:50.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:50.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:50.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:50.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:50.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:50.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:50.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:50.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:50.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:50.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:50.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:50.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:50.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:50.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:50.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:50.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:50.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:50.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:50.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:50.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:50.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:50.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:50.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:50.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:50.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:50.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:21:50.976][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-05-29 19:21:50.977][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:50.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:50.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:50.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:50.981][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:50.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:50.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:50.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:50.987][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:50.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:50.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:50.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:50.992][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:50.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:50.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:50.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:50.997][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:50.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:50.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:51.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:21:51.001][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:51.002][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:51.003][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:51.010][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:51.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:51.012][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:51.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:51.015][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-05-29 19:21:51.017][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-29 19:21:51.019][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-05-29 19:21:51.020][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-29 19:21:51.021][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-29 19:21:51.022][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-29 19:21:51.023][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-29 19:21:51.024][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-29 19:21:51.025][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-29 19:21:51.029][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:51.030][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:51.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:51.039][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:51.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:51.042][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:51.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:51.045][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-05-29 19:21:51.048][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:21:51.050][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:21:51.052][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-05-29 19:21:51.390][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-05-29 19:21:51.728][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:21:51.731][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-05-29 19:21:51.736][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-05-29 19:21:51.789][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-05-29 19:21:51.791][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-29 19:21:51.793][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-29 19:21:51.794][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-29 19:21:51.797][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:51.798][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:51.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:51.817][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:51.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:51.820][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:51.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:21:51.824][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:51.826][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:51.828][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:51.829][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:51.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:51.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:51.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:51.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:51.836][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:21:51.838][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:21:51.839][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:51.840][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:51.842][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:21:51.843][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:21:51.845][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:51.846][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:51.848][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:21:51.849][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:21:51.850][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:51.852][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:51.853][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:21:51.854][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:21:51.856][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:51.857][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:51.858][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:51.860][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:51.861][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:51.863][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:51.865][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:21:51.866][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:51.867][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:51.868][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:51.870][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:51.871][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:51.872][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:51.874][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:51.875][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:51.877][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:51.878][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:51.879][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:51.882][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:51.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:51.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:51.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:51.886][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:21:51.888][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:21:51.889][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:51.890][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:51.892][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:21:51.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:21:51.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:51.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:51.897][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:21:51.898][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:21:51.900][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:51.901][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:51.903][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:51.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:51.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:51.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:51.908][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:51.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:51.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:51.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:51.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:51.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:51.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:51.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:51.918][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:51.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:51.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:51.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:51.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:51.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:51.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:51.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:51.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:51.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:51.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:51.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:51.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:51.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:51.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:51.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:51.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:51.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:51.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:51.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:51.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:51.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:51.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:51.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:51.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:51.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:51.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:51.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:21:51.959][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-05-29 19:21:51.960][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:51.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:51.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:51.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:51.965][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:51.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:51.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:51.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:51.970][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:51.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:51.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:51.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:51.975][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:51.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:51.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:51.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:51.979][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:51.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:51.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:51.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:21:51.983][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:51.984][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:51.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:51.993][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:51.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:51.995][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:51.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:51.997][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-05-29 19:21:51.998][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-29 19:21:52.000][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-05-29 19:21:52.002][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-29 19:21:52.003][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-29 19:21:52.004][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-29 19:21:52.005][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-29 19:21:52.007][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-29 19:21:52.008][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-29 19:21:52.012][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:52.013][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:52.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:52.021][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:52.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:52.023][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:52.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:52.026][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-05-29 19:21:52.029][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:21:52.030][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:21:52.033][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-05-29 19:21:52.375][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-05-29 19:21:52.716][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:21:52.719][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-05-29 19:21:52.725][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-05-29 19:21:52.729][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-05-29 19:21:52.731][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-29 19:21:52.733][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-29 19:21:52.735][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-29 19:21:52.737][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:52.738][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:52.739][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:52.747][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:52.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:52.749][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:52.751][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[2024-05-29 19:21:52.754][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:52.755][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:52.757][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:52.758][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:52.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:52.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:52.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:52.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:52.765][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:21:52.767][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:21:52.768][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:52.769][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:52.771][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:21:52.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:21:52.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:52.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:52.776][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:21:52.778][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:21:52.779][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:52.781][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:52.783][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:21:52.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:21:52.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:52.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:52.798][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:21:52.800][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:21:52.802][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:52.803][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:52.805][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:21:52.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:21:52.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:52.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:52.811][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:21:52.812][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:21:52.814][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:52.816][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:52.818][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:21:52.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:21:52.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:52.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:52.823][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:52.824][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:52.825][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:52.826][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:52.828][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:52.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:52.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:52.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:52.832][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:21:52.833][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:52.834][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:52.836][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:52.837][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:21:52.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:52.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:52.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:52.841][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:52.843][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:52.844][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:52.845][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:52.847][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:52.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:52.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:52.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:52.852][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:52.853][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:52.853][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:52.854][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:52.856][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:52.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:52.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:52.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:52.861][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:21:52.863][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:21:52.864][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:52.865][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:52.867][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:21:52.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:21:52.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:52.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:52.873][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:21:52.874][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:21:52.874][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:52.875][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:52.877][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:21:52.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:21:52.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:52.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:52.881][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:52.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:52.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:52.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:52.885][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:52.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:52.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:52.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:52.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:52.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:52.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:52.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:52.895][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:52.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:52.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:52.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:52.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:52.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:52.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:52.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:52.903][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:52.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:52.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:52.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:52.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:52.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:52.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:52.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:52.911][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:52.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:52.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:52.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:52.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:52.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:52.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:52.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:52.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:52.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:52.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:52.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:21:52.923][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-05-29 19:21:52.924][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:52.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:52.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:52.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:52.927][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:52.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:52.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:52.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:52.938][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:52.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:52.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:52.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:21:52.945][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:52.946][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:52.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:52.953][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:52.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:52.955][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:52.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:52.957][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-05-29 19:21:52.959][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-29 19:21:52.960][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-05-29 19:21:52.962][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-29 19:21:52.964][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-29 19:21:52.965][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-29 19:21:52.967][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-29 19:21:52.968][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-29 19:21:52.969][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-29 19:21:52.972][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:52.973][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:52.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:52.983][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:52.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:52.985][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:52.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:52.987][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-05-29 19:21:52.990][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:21:52.992][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:21:52.994][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-05-29 19:21:53.330][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-05-29 19:21:53.670][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:21:53.673][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-05-29 19:21:53.678][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-05-29 19:21:53.682][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-05-29 19:21:53.684][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-29 19:21:53.686][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-29 19:21:53.688][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-29 19:21:53.690][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:53.691][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:53.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:53.702][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:53.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:53.705][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:53.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:21:53.710][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:53.712][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:53.713][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:53.715][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:53.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:53.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:53.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:53.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:53.722][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:21:53.724][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:21:53.725][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:53.726][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:53.727][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:21:53.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:21:53.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:53.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:53.732][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:21:53.734][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:21:53.735][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:53.737][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:53.739][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:21:53.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:21:53.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:53.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:53.744][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:21:53.745][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:21:53.746][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:53.747][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:53.749][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:21:53.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:21:53.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:53.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:53.754][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:21:53.755][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:21:53.757][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:53.758][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:53.760][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:21:53.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:21:53.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:53.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:53.765][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:53.778][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:53.780][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:53.782][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:53.785][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:53.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:53.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:53.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:53.792][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:21:53.794][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:53.795][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:53.796][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:53.798][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:21:53.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:53.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:53.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:53.801][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:53.802][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:53.804][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:53.806][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:53.808][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:53.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:53.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:53.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:53.813][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:53.815][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:53.816][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:53.817][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:53.821][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:53.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:53.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:53.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:53.827][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:21:53.828][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:21:53.829][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:53.830][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:53.832][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:21:53.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:21:53.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:53.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:53.838][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:21:53.839][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:21:53.840][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:53.841][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:53.843][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:21:53.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:21:53.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:53.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:53.849][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:53.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:53.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:53.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:53.854][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:53.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:53.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:53.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:53.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:53.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:53.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:53.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:53.865][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:53.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:53.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:53.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:53.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:53.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:53.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:53.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:53.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:53.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:53.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:53.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:53.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:53.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:53.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:53.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:53.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:53.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:53.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:53.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:53.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:53.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:53.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:53.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:53.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:53.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:53.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:53.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:21:53.902][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-05-29 19:21:53.903][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:53.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:53.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:53.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:53.908][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:53.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:53.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:53.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:53.912][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:53.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:53.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:53.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:21:53.916][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:53.917][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:53.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:53.926][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:53.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:53.929][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:53.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:53.938][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-05-29 19:21:53.940][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-29 19:21:53.942][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-05-29 19:21:53.943][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-29 19:21:53.944][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-29 19:21:53.946][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-29 19:21:53.947][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-29 19:21:53.948][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-29 19:21:53.949][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-29 19:21:53.954][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:53.956][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:53.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:53.964][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:53.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:53.967][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:53.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:53.969][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-05-29 19:21:53.972][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:21:53.973][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:21:53.975][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-05-29 19:21:54.314][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-05-29 19:21:54.654][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:21:54.657][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-05-29 19:21:54.662][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-05-29 19:21:54.665][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-05-29 19:21:54.667][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-29 19:21:54.668][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-29 19:21:54.670][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-29 19:21:54.688][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:54.689][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:54.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:54.699][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:54.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:54.706][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:54.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:21:54.713][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:54.715][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:54.716][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:54.718][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:54.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:54.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:54.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:54.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:54.724][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:21:54.725][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:21:54.726][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:54.728][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:54.730][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:21:54.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:21:54.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:54.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:54.735][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:21:54.737][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:21:54.738][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:54.739][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:54.741][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:21:54.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:21:54.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:54.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:54.746][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:21:54.748][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:21:54.750][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:54.751][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:54.753][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:21:54.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:21:54.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:54.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:54.758][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:21:54.759][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:21:54.760][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:54.761][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:54.763][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:21:54.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:21:54.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:54.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:54.767][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:54.768][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:54.769][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:54.771][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:54.772][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:21:54.773][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:54.775][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:54.776][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:54.778][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:21:54.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:54.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:54.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:54.783][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:54.785][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:54.787][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:54.788][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:54.790][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:54.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:54.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:54.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:54.806][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:54.808][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:54.809][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:54.811][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:54.813][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:54.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:54.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:54.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:54.818][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:21:54.820][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:21:54.821][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:54.822][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:54.823][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:21:54.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:21:54.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:54.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:54.828][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:21:54.829][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:21:54.830][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:54.831][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:54.833][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:21:54.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:21:54.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:54.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:54.838][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:54.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:54.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:54.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:54.843][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:54.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:54.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:54.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:54.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:54.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:54.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:54.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:54.853][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:54.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:54.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:54.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:54.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:54.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:54.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:54.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:54.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:54.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:54.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:54.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:54.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:54.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:54.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:54.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:54.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:54.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:54.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:54.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:54.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:54.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:54.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:54.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:54.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:54.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:54.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:54.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:21:54.891][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-05-29 19:21:54.893][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:54.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:54.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:54.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:54.898][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:54.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:54.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:54.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:54.902][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:54.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:54.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:54.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:21:54.907][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:54.909][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:54.910][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:54.918][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:54.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:54.921][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:54.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:54.924][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-05-29 19:21:54.926][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-29 19:21:54.928][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-05-29 19:21:54.930][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-29 19:21:54.931][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-29 19:21:54.933][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-29 19:21:54.934][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-29 19:21:54.935][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-29 19:21:54.937][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-29 19:21:54.940][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:54.941][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:54.943][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:54.950][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:54.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:54.953][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:54.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:54.962][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-05-29 19:21:54.968][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:21:54.969][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:21:54.971][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-05-29 19:21:55.315][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-05-29 19:21:55.653][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:21:55.657][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-05-29 19:21:55.662][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-05-29 19:21:55.666][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-05-29 19:21:55.668][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-29 19:21:55.670][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-29 19:21:55.672][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-29 19:21:55.674][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:55.675][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:55.677][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:55.684][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:55.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:55.687][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:55.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:21:55.691][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:55.693][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:55.695][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:55.696][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:55.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:55.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:55.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:55.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:55.703][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:21:55.705][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:21:55.706][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:55.707][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:55.709][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:21:55.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:21:55.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:55.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:55.714][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:21:55.715][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:21:55.716][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:55.717][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:55.719][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:21:55.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:21:55.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:55.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:55.726][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:21:55.727][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:21:55.728][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:55.730][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:55.731][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:21:55.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:21:55.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:55.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:55.736][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:21:55.737][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:21:55.738][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:55.739][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:55.741][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:21:55.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:21:55.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:55.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:55.747][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:55.749][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:55.750][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:55.751][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:55.753][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:21:55.755][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:55.756][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:55.757][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:55.759][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:21:55.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:55.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:55.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:55.764][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:55.765][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:55.767][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:55.768][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:55.770][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:55.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:55.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:55.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:55.777][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:55.778][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:55.779][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:55.781][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:55.783][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:55.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:55.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:55.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:55.788][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:21:55.790][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:21:55.791][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:55.792][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:55.794][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:21:55.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:21:55.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:55.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:55.799][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:21:55.806][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:21:55.812][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:55.814][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:55.816][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:21:55.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:21:55.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:55.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:55.820][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:55.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:55.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:55.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:55.826][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:55.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:55.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:55.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:55.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:55.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:55.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:55.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:55.833][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:55.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:55.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:55.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:55.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:55.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:55.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:55.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:55.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:55.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:55.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:55.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:55.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:55.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:55.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:55.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:55.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:55.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:55.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:55.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:55.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:55.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:55.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:55.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:55.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:55.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:55.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:55.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:21:55.871][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-05-29 19:21:55.872][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:55.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:55.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:55.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:55.878][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:55.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:55.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:55.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:55.883][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:55.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:55.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:55.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:21:55.889][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:55.890][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:55.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:55.898][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:55.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:55.901][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:55.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:55.903][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-05-29 19:21:55.905][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-29 19:21:55.907][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-05-29 19:21:55.909][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-29 19:21:55.910][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-29 19:21:55.912][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-29 19:21:55.914][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-29 19:21:55.915][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-29 19:21:55.916][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-29 19:21:55.919][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:55.920][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:55.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:55.929][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:55.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:55.931][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:55.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:55.934][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-05-29 19:21:55.937][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:21:55.938][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:21:55.939][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-05-29 19:21:56.281][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-05-29 19:21:56.633][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:21:56.636][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-05-29 19:21:56.641][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-05-29 19:21:56.643][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-05-29 19:21:56.646][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-29 19:21:56.647][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-29 19:21:56.649][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-29 19:21:56.661][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:56.663][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:56.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:56.672][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:56.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:56.675][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:56.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:21:56.679][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:56.681][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:56.682][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:56.683][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:56.684][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:56.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:56.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:56.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:56.688][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:21:56.689][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:21:56.690][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:56.692][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:56.693][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:21:56.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:21:56.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:56.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:56.698][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:21:56.700][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:21:56.701][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:56.703][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:56.704][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:21:56.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:21:56.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:56.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:56.708][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:21:56.709][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:21:56.710][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:56.711][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:56.713][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:21:56.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:21:56.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:56.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:56.718][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:21:56.719][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:21:56.721][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:56.722][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:56.724][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:21:56.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:21:56.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:56.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:56.729][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:56.730][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:56.731][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:56.732][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:56.734][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:21:56.736][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:56.737][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:56.738][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:56.740][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:21:56.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:56.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:56.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:56.746][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:56.747][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:56.748][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:56.749][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:56.750][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:56.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:56.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:56.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:56.755][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:56.756][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:56.758][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:56.758][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:56.760][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:56.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:56.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:56.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:56.764][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:21:56.765][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:21:56.766][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:56.767][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:56.769][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:21:56.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:21:56.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:56.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:56.774][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:21:56.776][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:21:56.776][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:56.777][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:56.779][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:21:56.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:21:56.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:56.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:56.783][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:56.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:56.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:56.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:56.788][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:56.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:56.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:56.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:56.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:56.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:56.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:56.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:56.798][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:56.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:56.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:56.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:56.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:56.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:56.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:56.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:56.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:56.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:56.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:56.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:56.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:56.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:56.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:56.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:56.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:56.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:56.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:56.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:56.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:56.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:56.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:56.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:56.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:56.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:56.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:56.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:21:56.841][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-05-29 19:21:56.842][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:56.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:56.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:56.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:56.847][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:56.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:56.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:56.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:56.852][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:56.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:56.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:56.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:21:56.857][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:56.858][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:56.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:56.865][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:56.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:56.867][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:56.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:56.870][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-05-29 19:21:56.872][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-29 19:21:56.874][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-05-29 19:21:56.875][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-29 19:21:56.876][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-29 19:21:56.877][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-29 19:21:56.878][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-29 19:21:56.880][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-29 19:21:56.881][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-29 19:21:56.884][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:56.885][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:56.886][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:56.893][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:56.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:56.895][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:56.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:56.898][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2024-05-29 19:21:56.901][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:21:56.901][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:21:56.903][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-05-29 19:21:57.245][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2024-05-29 19:21:57.586][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:21:57.589][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-05-29 19:21:57.594][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-05-29 19:21:57.598][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-05-29 19:21:57.600][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-29 19:21:57.601][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-29 19:21:57.603][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-29 19:21:57.604][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:57.606][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:57.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:57.615][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:57.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:57.617][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:57.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:21:57.622][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:57.623][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:57.624][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:57.626][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:57.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:57.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:57.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:57.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:57.642][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:21:57.644][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:21:57.645][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:57.646][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:57.647][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:21:57.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:21:57.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:57.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:57.651][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:21:57.652][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:21:57.653][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:57.654][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:57.655][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:21:57.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:21:57.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:57.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:57.661][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:21:57.662][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:21:57.663][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:57.665][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:57.666][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:21:57.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:21:57.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:57.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:57.670][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:21:57.671][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:21:57.672][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:57.674][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:57.675][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:21:57.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:21:57.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:57.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:57.681][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:57.682][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:57.683][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:57.684][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:57.686][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:21:57.687][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:57.688][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:57.689][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:57.691][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:21:57.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:57.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:57.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:57.697][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:57.698][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:57.699][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:57.701][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:57.702][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:57.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:57.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:57.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:57.708][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:57.709][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:57.711][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:57.712][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:57.714][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:57.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:57.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:57.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:57.719][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:21:57.720][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:21:57.721][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:57.722][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:57.723][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:21:57.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:21:57.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:57.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:57.729][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:21:57.731][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:21:57.731][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:57.733][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:57.734][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:21:57.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:21:57.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:57.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:57.739][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:57.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:57.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:57.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:57.744][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:57.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:57.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:57.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:57.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:57.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:57.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:57.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:57.755][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:57.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:57.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:57.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:57.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:57.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:57.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:57.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:57.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:57.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:57.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:57.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:57.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:57.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:57.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:57.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:57.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:57.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:57.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:57.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:57.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:57.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:57.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:57.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:57.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:57.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:57.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:57.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:21:57.792][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-05-29 19:21:57.793][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:57.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:57.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:57.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:57.798][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:57.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:57.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:57.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:57.802][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:57.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:57.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:57.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:21:57.807][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:57.808][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:57.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:57.817][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:57.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:57.820][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:57.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:57.822][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-05-29 19:21:57.823][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-29 19:21:57.825][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-05-29 19:21:57.827][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-29 19:21:57.828][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-29 19:21:57.829][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-29 19:21:57.831][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-29 19:21:57.832][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-29 19:21:57.833][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-29 19:21:57.836][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:57.837][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:57.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:57.845][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:57.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:57.848][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:57.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:57.851][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2024-05-29 19:21:57.856][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:21:57.857][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:21:57.859][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2024-05-29 19:21:58.200][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2024-05-29 19:21:58.539][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:21:58.542][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2024-05-29 19:21:58.547][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2024-05-29 19:21:58.551][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2024-05-29 19:21:58.552][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-29 19:21:58.554][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-29 19:21:58.555][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-29 19:21:58.558][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:58.559][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:58.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:58.568][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:58.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:58.570][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:58.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:21:58.574][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:58.575][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:58.576][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:58.578][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:58.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:58.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:58.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:58.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:58.585][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:21:58.586][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:21:58.587][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:58.589][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:58.590][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:21:58.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:21:58.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:58.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:58.595][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:21:58.596][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:21:58.598][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:58.598][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:58.600][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:21:58.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:21:58.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:58.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:58.604][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:21:58.606][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:21:58.620][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:58.622][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:58.624][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:21:58.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:21:58.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:58.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:58.630][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:21:58.631][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:21:58.632][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:58.634][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:58.635][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:21:58.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:21:58.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:58.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:58.641][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:58.642][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:58.644][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:58.645][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:58.647][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:21:58.649][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:58.650][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:58.651][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:58.652][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:21:58.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:58.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:58.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:58.656][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:58.657][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:58.658][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:58.659][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:58.660][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:58.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:58.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:58.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:58.665][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:58.666][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:58.667][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:58.669][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:58.671][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:58.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:58.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:58.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:58.675][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:21:58.676][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:21:58.677][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:58.678][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:58.680][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:21:58.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:21:58.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:58.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:58.684][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:21:58.686][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:21:58.687][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:58.688][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:58.690][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:21:58.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:21:58.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:58.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:58.695][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:58.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:58.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:58.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:58.701][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:58.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:58.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:58.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:58.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:58.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:58.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:58.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:58.711][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:58.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:58.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:58.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:58.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:58.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:58.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:58.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:58.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:58.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:58.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:58.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:58.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:58.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:58.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:58.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:58.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:58.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:58.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:58.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:58.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:58.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:58.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:58.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:58.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:58.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:58.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:58.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:21:58.745][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-05-29 19:21:58.747][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:58.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:58.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:58.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:58.753][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:58.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:58.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:58.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:58.758][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:58.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:58.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:58.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:21:58.771][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:58.772][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:58.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:58.780][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:58.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:58.783][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:58.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:58.786][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-05-29 19:21:58.787][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-29 19:21:58.789][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-05-29 19:21:58.790][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-29 19:21:58.792][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-29 19:21:58.793][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-29 19:21:58.795][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-29 19:21:58.796][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-29 19:21:58.797][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-29 19:21:58.801][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:58.802][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:58.803][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:58.810][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:58.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:58.812][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:58.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:58.815][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2024-05-29 19:21:58.817][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:21:58.818][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:21:58.820][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2024-05-29 19:21:59.159][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2024-05-29 19:21:59.498][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:21:59.502][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2024-05-29 19:21:59.507][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2024-05-29 19:21:59.510][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2024-05-29 19:21:59.513][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-29 19:21:59.514][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-29 19:21:59.516][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-29 19:21:59.518][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:59.519][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:59.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:59.528][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:59.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:59.531][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:59.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:21:59.535][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:59.536][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:59.538][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:59.539][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:59.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:59.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:59.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:59.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:59.545][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:21:59.546][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:21:59.548][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:59.549][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:59.551][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:21:59.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:21:59.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:59.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:59.556][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:21:59.558][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:21:59.559][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:59.560][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:59.562][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:21:59.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:21:59.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:59.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:59.568][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:21:59.570][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:21:59.571][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:59.572][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:59.573][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:21:59.575][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:21:59.576][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:59.577][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:59.579][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:59.580][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:21:59.582][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:59.583][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:59.585][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:21:59.586][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:59.587][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:59.588][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:59.590][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:21:59.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:59.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:59.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:59.607][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:59.609][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:59.610][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:59.612][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:59.613][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:59.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:21:59.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:59.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:59.619][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:59.620][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:59.622][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:59.622][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:59.625][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:21:59.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:21:59.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:59.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:59.629][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:21:59.631][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:21:59.632][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:59.633][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:59.635][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:21:59.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:21:59.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:59.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:59.639][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:21:59.641][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:21:59.642][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:59.643][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:59.645][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:59.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:59.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:59.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:59.651][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:59.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:59.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:59.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:59.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:59.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:59.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:59.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:59.662][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:21:59.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:21:59.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:59.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:59.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:59.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:59.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:59.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:59.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:59.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:59.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:59.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:59.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:59.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:59.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:59.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:59.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:59.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:59.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:59.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:59.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:59.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:59.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:59.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:59.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:21:59.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:21:59.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:59.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:21:59.697][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-05-29 19:21:59.699][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:59.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:59.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:59.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:59.704][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:59.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:59.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:59.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:21:59.709][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:59.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:21:59.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:21:59.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:21:59.715][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:59.716][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:59.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:59.723][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:59.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:59.726][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:59.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:59.728][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-05-29 19:21:59.729][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-29 19:21:59.731][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-05-29 19:21:59.733][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-29 19:21:59.735][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-29 19:21:59.736][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-29 19:21:59.738][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-29 19:21:59.739][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-29 19:21:59.740][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-29 19:21:59.744][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:21:59.745][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:21:59.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:21:59.761][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:21:59.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:21:59.764][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:21:59.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:21:59.768][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2024-05-29 19:21:59.771][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:21:59.773][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:21:59.775][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2024-05-29 19:22:00.113][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2024-05-29 19:22:00.480][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:22:00.483][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2024-05-29 19:22:00.488][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2024-05-29 19:22:00.492][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2024-05-29 19:22:00.495][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-29 19:22:00.497][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-29 19:22:00.498][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-29 19:22:00.501][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:00.503][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:00.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:00.511][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:00.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:00.514][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:00.515][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[2024-05-29 19:22:00.518][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:00.519][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:00.520][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:00.521][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:00.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:00.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:00.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:00.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:00.528][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:22:00.530][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:22:00.531][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:00.531][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:00.533][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:22:00.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:22:00.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:00.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:00.538][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:22:00.540][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:22:00.541][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:00.543][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:00.544][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:22:00.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:22:00.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:00.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:00.548][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:22:00.549][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:22:00.550][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:00.552][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:00.553][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:22:00.555][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:22:00.556][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:00.557][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:00.559][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:00.560][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:00.562][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:00.563][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:00.564][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:22:00.565][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:00.567][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:00.567][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:00.569][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:22:00.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:00.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:00.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:00.574][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:00.575][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:00.577][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:00.578][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:00.579][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:00.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:00.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:00.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:00.584][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:00.585][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:00.586][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:00.587][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:00.589][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:00.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:00.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:00.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:00.593][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:22:00.594][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:22:00.595][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:00.596][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:00.598][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:22:00.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:22:00.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:00.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:00.602][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:22:00.604][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:22:00.606][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:00.608][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:00.623][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:00.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:00.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:00.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:00.629][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:00.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:00.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:00.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:00.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:00.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:00.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:00.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:00.637][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:00.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:00.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:00.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:00.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:00.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:00.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:00.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:00.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:00.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:00.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:00.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:00.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:00.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:00.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:00.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:00.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:00.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:00.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:00.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:00.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:00.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:00.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:00.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:00.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:00.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:00.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:00.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:00.666][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-05-29 19:22:00.668][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:00.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:00.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:00.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:00.674][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:00.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:00.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:00.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:00.679][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:00.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:00.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:00.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:00.683][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:00.685][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:00.686][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:00.692][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:00.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:00.694][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:00.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:00.696][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-05-29 19:22:00.697][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-29 19:22:00.698][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-05-29 19:22:00.700][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-29 19:22:00.702][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-29 19:22:00.703][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-29 19:22:00.704][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-29 19:22:00.705][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-29 19:22:00.706][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-29 19:22:00.710][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:00.711][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:00.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:00.720][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:00.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:00.723][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:00.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:00.726][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2024-05-29 19:22:00.728][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:22:00.730][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:22:00.732][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2024-05-29 19:22:01.073][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2024-05-29 19:22:01.424][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:22:01.427][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2024-05-29 19:22:01.432][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2024-05-29 19:22:01.437][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2024-05-29 19:22:01.439][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-29 19:22:01.441][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-29 19:22:01.443][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-29 19:22:01.445][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:01.446][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:01.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:01.468][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:01.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:01.471][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:01.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:01.475][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:01.477][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:01.479][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:01.480][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:01.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:01.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:01.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:01.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:01.491][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:22:01.492][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:22:01.494][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:01.495][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:01.497][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:22:01.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:22:01.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:01.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:01.502][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:22:01.504][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:22:01.505][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:01.506][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:01.508][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:22:01.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:22:01.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:01.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:01.514][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:22:01.515][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:22:01.517][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:01.518][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:01.519][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:22:01.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:22:01.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:01.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:01.525][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:22:01.527][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:22:01.528][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:01.530][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:01.531][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:22:01.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:22:01.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:01.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:01.536][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:01.537][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:01.539][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:01.540][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:01.542][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:22:01.544][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:01.545][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:01.547][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:01.548][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:22:01.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:01.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:01.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:01.553][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:01.555][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:01.556][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:01.557][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:01.559][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:01.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:01.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:01.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:01.565][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:01.567][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:01.568][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:01.569][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:01.571][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:01.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:01.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:01.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:01.577][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:22:01.579][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:22:01.580][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:01.582][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:01.584][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:22:01.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:22:01.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:01.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:01.589][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:22:01.590][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:22:01.591][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:01.593][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:01.594][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:22:01.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:22:01.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:01.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:01.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:01.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:01.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:01.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:01.605][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:01.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:01.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:01.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:01.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:01.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:01.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:01.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:01.616][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:01.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:01.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:01.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:01.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:01.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:01.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:01.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:01.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:01.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:01.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:01.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:01.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:01.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:01.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:01.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:01.647][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:01.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:01.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:01.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:01.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:01.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:01.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:01.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:01.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:01.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:01.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:01.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:01.664][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-05-29 19:22:01.665][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:01.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:01.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:01.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:01.670][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:01.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:01.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:01.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:01.675][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:01.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:01.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:01.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:01.681][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:01.682][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:01.683][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:01.691][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:01.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:01.694][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:01.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:01.696][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-05-29 19:22:01.698][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-29 19:22:01.700][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-05-29 19:22:01.702][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-29 19:22:01.703][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-29 19:22:01.705][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-29 19:22:01.706][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-29 19:22:01.707][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-29 19:22:01.709][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-29 19:22:01.713][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:01.714][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:01.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:01.723][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:01.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:01.726][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:01.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:01.729][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2024-05-29 19:22:01.732][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:22:01.734][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:22:01.736][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2024-05-29 19:22:02.076][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2024-05-29 19:22:02.419][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:22:02.422][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2024-05-29 19:22:02.428][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2024-05-29 19:22:02.432][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2024-05-29 19:22:02.435][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-29 19:22:02.437][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-29 19:22:02.439][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-29 19:22:02.441][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:02.442][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:02.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:02.450][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:02.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:02.453][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:02.455][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.TRACE[2024-05-29 19:22:02.458][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:02.460][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:02.461][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:02.462][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:02.464][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:02.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:02.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:02.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:02.470][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:22:02.478][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:22:02.485][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:02.487][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:02.489][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:22:02.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:22:02.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:02.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:02.495][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:22:02.497][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:22:02.498][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:02.499][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:02.501][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:22:02.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:22:02.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:02.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:02.506][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:22:02.507][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:22:02.509][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:02.510][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:02.512][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:22:02.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:22:02.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:02.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:02.518][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:22:02.519][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:22:02.520][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:02.522][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:02.523][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:22:02.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:22:02.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:02.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:02.528][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:02.530][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:02.531][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:02.532][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:02.533][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:22:02.534][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:02.535][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:02.536][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:02.537][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:22:02.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:02.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:02.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:02.541][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:02.542][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:02.543][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:02.544][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:02.545][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:02.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:02.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:02.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:02.549][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:02.551][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:02.552][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:02.553][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:02.555][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:02.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:02.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:02.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:02.559][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:22:02.561][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:22:02.562][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:02.563][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:02.565][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:22:02.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:22:02.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:02.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:02.570][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:22:02.572][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:22:02.573][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:02.574][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:02.576][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:22:02.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:22:02.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:02.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:02.582][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:02.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:02.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:02.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:02.587][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:02.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:02.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:02.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:02.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:02.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:02.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:02.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:02.596][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:02.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:02.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:02.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:02.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:02.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:02.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:02.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:02.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:02.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:02.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:02.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:02.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:02.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:02.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:02.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:02.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:02.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:02.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:02.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:02.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:02.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:02.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:02.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:02.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:02.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:02.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:02.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:02.640][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-05-29 19:22:02.641][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:02.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:02.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:02.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:02.647][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:02.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:02.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:02.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:02.652][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:02.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:02.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:02.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:02.657][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:02.659][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:02.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:02.667][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:02.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:02.670][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:02.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:02.673][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-05-29 19:22:02.675][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-29 19:22:02.677][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-05-29 19:22:02.679][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-29 19:22:02.681][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-29 19:22:02.682][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-29 19:22:02.683][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-29 19:22:02.685][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-29 19:22:02.686][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-29 19:22:02.690][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:02.691][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:02.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:02.700][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:02.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:02.703][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:02.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:02.706][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2024-05-29 19:22:02.710][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:22:02.712][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:22:02.714][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2024-05-29 19:22:03.071][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2024-05-29 19:22:03.411][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:22:03.414][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2024-05-29 19:22:03.420][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2024-05-29 19:22:03.424][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2024-05-29 19:22:03.426][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-29 19:22:03.428][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-29 19:22:03.430][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-29 19:22:03.432][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:03.434][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:03.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:03.443][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:03.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:03.445][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:03.447][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.TRACE[2024-05-29 19:22:03.450][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:03.452][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:03.453][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:03.455][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:03.456][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:03.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:03.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:03.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:03.462][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:22:03.464][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:22:03.465][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:03.466][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:03.468][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:22:03.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:22:03.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:03.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:03.474][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:22:03.475][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:22:03.477][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:03.478][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:03.480][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:22:03.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:22:03.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:03.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:03.485][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:22:03.487][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:22:03.496][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:03.503][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:03.505][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:22:03.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:22:03.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:03.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:03.512][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:22:03.513][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:22:03.515][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:03.516][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:03.518][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:22:03.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:22:03.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:03.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:03.523][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:03.525][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:03.526][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:03.527][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:03.529][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:22:03.531][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:03.532][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:03.533][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:03.535][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:22:03.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:03.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:03.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:03.561][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:03.579][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:03.581][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:03.582][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:03.603][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:03.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:03.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:03.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:03.609][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:03.611][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:03.612][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:03.613][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:03.616][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:03.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:03.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:03.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:03.621][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:22:03.622][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:22:03.624][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:03.625][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:03.627][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:22:03.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:22:03.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:03.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:03.652][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:22:03.653][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:22:03.655][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:03.656][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:03.658][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:22:03.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:22:03.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:03.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:03.664][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:03.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:03.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:03.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:03.688][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:03.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:03.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:03.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:03.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:03.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:03.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:03.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:03.699][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:03.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:03.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:03.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:03.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:03.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:03.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:03.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:03.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:03.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:03.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:03.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:03.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:03.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:03.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:03.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:03.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:03.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:03.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:03.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:03.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:03.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:03.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:03.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:03.750][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:03.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:03.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:03.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:03.755][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-05-29 19:22:03.757][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:03.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:03.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:03.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:03.762][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:03.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:03.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:03.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:03.768][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:03.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:03.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:03.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:03.787][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:03.790][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:03.791][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:03.799][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:03.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:03.802][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:03.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:03.805][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-05-29 19:22:03.806][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-29 19:22:03.817][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-05-29 19:22:03.819][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-29 19:22:03.821][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-29 19:22:03.822][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-29 19:22:03.833][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-29 19:22:03.836][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-29 19:22:03.839][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-29 19:22:03.843][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:03.859][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:03.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:03.874][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:03.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:03.878][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:03.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:03.881][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2024-05-29 19:22:03.895][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:22:03.897][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:22:03.899][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2024-05-29 19:22:04.271][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2024-05-29 19:22:04.613][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:22:04.616][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2024-05-29 19:22:04.622][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2024-05-29 19:22:04.626][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2024-05-29 19:22:04.629][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-29 19:22:04.631][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-29 19:22:04.633][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-29 19:22:04.635][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:04.637][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:04.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:04.646][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:04.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:04.649][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:04.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:04.653][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:04.655][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:04.656][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:04.658][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:04.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:04.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:04.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:04.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:04.666][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:22:04.667][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:22:04.669][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:04.670][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:04.672][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:22:04.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:22:04.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:04.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:04.678][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:22:04.679][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:22:04.681][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:04.682][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:04.684][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:22:04.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:22:04.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:04.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:04.689][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:22:04.691][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:22:04.692][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:04.693][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:04.695][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:22:04.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:22:04.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:04.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:04.700][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:22:04.702][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:22:04.703][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:04.704][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:04.706][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:22:04.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:22:04.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:04.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:04.712][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:04.713][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:04.714][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:04.715][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:04.717][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:22:04.732][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:04.733][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:04.735][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:04.737][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:22:04.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:04.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:04.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:04.743][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:04.745][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:04.746][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:04.747][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:04.749][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:04.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:04.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:04.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:04.754][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:04.756][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:04.757][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:04.758][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:04.760][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:04.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:04.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:04.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:04.765][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:22:04.767][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:22:04.768][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:04.769][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:04.771][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:22:04.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:22:04.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:04.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:04.776][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:22:04.778][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:22:04.779][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:04.780][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:04.782][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:22:04.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:22:04.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:04.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:04.788][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:04.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:04.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:04.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:04.793][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:04.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:04.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:04.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:04.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:04.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:04.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:04.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:04.803][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:04.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:04.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:04.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:04.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:04.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:04.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:04.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:04.814][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:04.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:04.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:04.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:04.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:04.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:04.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:04.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:04.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:04.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:04.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:04.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:04.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:04.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:04.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:04.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:04.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:04.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:04.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:04.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:04.857][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-05-29 19:22:04.859][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:04.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:04.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:04.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:04.865][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:04.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:04.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:04.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:04.880][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:04.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:04.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:04.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:04.893][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:04.895][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:04.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:04.919][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:04.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:04.922][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:04.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:04.925][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-05-29 19:22:04.933][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-29 19:22:04.936][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-05-29 19:22:04.938][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-29 19:22:04.940][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-29 19:22:04.942][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-29 19:22:04.962][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-29 19:22:04.964][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-29 19:22:04.966][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-29 19:22:04.971][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:04.979][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:04.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:04.995][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:04.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:04.998][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:05.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:05.001][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2024-05-29 19:22:05.015][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:22:05.016][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:22:05.019][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2024-05-29 19:22:05.381][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2024-05-29 19:22:05.723][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:22:05.726][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2024-05-29 19:22:05.731][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2024-05-29 19:22:05.735][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2024-05-29 19:22:05.738][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-29 19:22:05.740][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-29 19:22:05.742][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-29 19:22:05.744][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:05.746][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:05.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:05.755][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:05.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:05.758][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:05.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:05.763][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:05.765][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:05.766][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:05.768][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:05.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:05.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:05.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:05.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:05.775][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:22:05.777][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:22:05.778][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:05.780][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:05.781][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:22:05.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:22:05.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:05.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:05.787][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:22:05.789][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:22:05.790][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:05.791][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:05.793][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:22:05.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:22:05.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:05.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:05.799][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:22:05.800][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:22:05.802][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:05.803][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:05.805][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:22:05.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:22:05.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:05.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:05.810][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:22:05.812][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:22:05.813][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:05.814][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:05.816][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:22:05.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:22:05.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:05.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:05.822][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:05.823][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:05.825][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:05.826][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:05.828][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:22:05.829][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:05.831][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:05.832][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:05.835][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:22:05.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:05.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:05.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:05.841][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:05.842][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:05.844][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:05.845][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:05.847][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:05.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:05.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:05.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:05.853][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:05.854][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:05.864][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:05.871][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:05.873][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:05.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:05.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:05.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:05.880][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:22:05.881][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:22:05.883][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:05.884][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:05.886][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:22:05.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:22:05.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:05.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:05.891][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:22:05.892][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:22:05.894][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:05.895][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:05.897][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:22:05.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:22:05.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:05.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:05.903][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:05.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:05.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:05.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:05.908][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:05.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:05.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:05.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:05.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:05.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:05.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:05.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:05.918][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:05.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:05.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:05.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:05.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:05.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:05.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:05.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:05.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:05.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:05.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:05.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:05.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:05.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:05.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:05.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:05.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:05.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:05.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:05.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:05.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:05.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:05.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:05.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:05.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:05.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:05.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:05.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:05.978][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-05-29 19:22:05.979][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:05.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:05.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:05.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:05.990][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:05.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:05.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:05.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:06.004][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:06.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:06.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:06.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:06.011][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:06.012][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:06.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:06.044][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:06.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:06.047][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:06.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:06.057][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-05-29 19:22:06.058][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-29 19:22:06.061][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-05-29 19:22:06.063][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-29 19:22:06.065][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-29 19:22:06.076][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-29 19:22:06.078][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-29 19:22:06.080][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-29 19:22:06.082][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-29 19:22:06.091][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:06.092][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:06.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:06.103][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:06.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:06.107][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:06.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:06.122][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2024-05-29 19:22:06.157][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:22:06.160][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:22:06.164][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2024-05-29 19:22:06.518][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2024-05-29 19:22:06.874][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:22:06.877][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2024-05-29 19:22:06.883][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2024-05-29 19:22:06.887][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2024-05-29 19:22:06.890][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-29 19:22:06.892][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-29 19:22:06.894][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-29 19:22:06.896][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:06.897][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:06.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:06.907][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:06.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:06.910][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:06.912][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[2024-05-29 19:22:06.915][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:06.917][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:06.918][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:06.919][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:06.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:06.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:06.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:06.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:06.927][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:22:06.929][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:22:06.930][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:06.932][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:06.933][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:22:06.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:22:06.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:06.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:06.939][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:22:06.941][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:22:06.942][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:06.943][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:06.945][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:22:06.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:22:06.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:06.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:06.951][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:22:06.953][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:22:06.954][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:06.955][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:06.957][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:22:06.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:22:06.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:06.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:06.963][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:22:06.964][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:22:06.966][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:06.967][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:06.969][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:22:06.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:22:06.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:06.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:06.975][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:06.976][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:06.978][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:06.979][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:06.981][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:22:06.982][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:06.984][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:06.985][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:06.987][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:22:06.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:06.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:06.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:06.993][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:06.994][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:06.995][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:06.997][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:06.999][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:07.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:07.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:07.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:07.005][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:07.006][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:07.007][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:07.009][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:07.011][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:07.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:07.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:07.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:07.017][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:22:07.018][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:22:07.020][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:07.021][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:07.023][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:22:07.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:22:07.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:07.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:07.029][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:22:07.030][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:22:07.032][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:07.041][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:07.048][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:22:07.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:22:07.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:07.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:07.056][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:07.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:07.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:07.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:07.062][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:07.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:07.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:07.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:07.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:07.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:07.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:07.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:07.074][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:07.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:07.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:07.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:07.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:07.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:07.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:07.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:07.098][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:07.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:07.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:07.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:07.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:07.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:07.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:07.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:07.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:07.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:07.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:07.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:07.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:07.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:07.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:07.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:07.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:07.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:07.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:07.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:07.154][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-05-29 19:22:07.157][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:07.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:07.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:07.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:07.170][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:07.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:07.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:07.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:07.186][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:07.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:07.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:07.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:07.198][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:07.200][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:07.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:07.210][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:07.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:07.213][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:07.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:07.217][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-05-29 19:22:07.226][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-29 19:22:07.229][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-05-29 19:22:07.232][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-29 19:22:07.233][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-29 19:22:07.235][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-29 19:22:07.245][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-29 19:22:07.246][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-29 19:22:07.248][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-29 19:22:07.252][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:07.260][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:07.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:07.282][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:07.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:07.285][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:07.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:07.296][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2024-05-29 19:22:07.301][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:22:07.303][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:22:07.306][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2024-05-29 19:22:07.658][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2024-05-29 19:22:08.000][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:22:08.004][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2024-05-29 19:22:08.009][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2024-05-29 19:22:08.014][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2024-05-29 19:22:08.017][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-29 19:22:08.019][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-29 19:22:08.021][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-29 19:22:08.038][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:08.041][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:08.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:08.051][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:08.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:08.054][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:08.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:08.059][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:08.061][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:08.062][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.064][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:08.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:08.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.071][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:22:08.073][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:22:08.074][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.075][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.077][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:22:08.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:22:08.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.082][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:22:08.084][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:22:08.085][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.086][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.088][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:22:08.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:22:08.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.094][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:22:08.095][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:22:08.097][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.098][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.099][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:22:08.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:22:08.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.105][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:22:08.106][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:22:08.108][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.109][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.111][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:22:08.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:22:08.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.116][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:08.117][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:08.119][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.120][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.122][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:22:08.123][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.124][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.126][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.127][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:22:08.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.133][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:08.134][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:08.135][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.137][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.138][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:08.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:08.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.144][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:08.145][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:08.146][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.147][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.149][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:08.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:08.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.155][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:22:08.156][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:22:08.157][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.158][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.160][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:22:08.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:22:08.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.165][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:22:08.167][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:22:08.168][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.169][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.171][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:22:08.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:22:08.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.177][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:08.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:08.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:08.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:08.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:08.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:08.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.206][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:08.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:08.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:08.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:08.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:08.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:08.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:08.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:08.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:08.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:08.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:08.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:08.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:08.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:08.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:08.294][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-05-29 19:22:08.296][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.309][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.316][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:08.374][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-29 19:22:08.398][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-29 19:22:08.401][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-29 19:22:08.403][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-29 19:22:08.405][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-05-29 19:22:08.415][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:08.417][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:08.419][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:08.432][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:08.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:08.435][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:08.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:08.438][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.462][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.475][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:08.492][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:08.494][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:08.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:08.506][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:08.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:08.509][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:08.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:08.512][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.527][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.539][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.563][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.578][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:08.594][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:08.595][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:08.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:08.613][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:08.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:08.616][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:08.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:08.619][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.633][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.646][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.653][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.665][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:08.677][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:08.679][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:08.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:08.688][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:08.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:08.691][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:08.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:08.694][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.711][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.731][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.738][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.752][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:08.764][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:08.766][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:08.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:08.786][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:08.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:08.791][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:08.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:08.794][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.804][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.819][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:08.825][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:08.827][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:08.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:08.843][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:08.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:08.846][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:08.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:08.849][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.865][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.900][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:08.913][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:08.915][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:08.917][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:08.935][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:08.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:08.938][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:08.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:08.941][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.957][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:08.972][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:08.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:08.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:08.978][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:08.987][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:08.989][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:08.997][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:08.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:09.001][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:09.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:09.004][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:09.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:09.019][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:09.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:09.034][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:09.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:09.040][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:09.049][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:09.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:09.060][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:09.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:09.063][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:09.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:09.066][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:09.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:09.080][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:09.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:09.096][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:09.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:09.116][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:09.118][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:09.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:09.131][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:09.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:09.135][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:09.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:09.144][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:09.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:09.154][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:09.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:09.171][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:09.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:09.189][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:09.190][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:09.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:09.218][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:09.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:09.222][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:09.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:09.235][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:09.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:09.248][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:09.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:09.290][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:09.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:09.308][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:09.310][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:09.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:09.321][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:09.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:09.325][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:09.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:09.342][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:09.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:09.360][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:09.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:09.368][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:09.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:09.384][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:09.386][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:09.394][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:09.417][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:09.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:09.421][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:09.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:09.432][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:09.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:09.438][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:09.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:09.454][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:09.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:09.468][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:09.469][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:09.471][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:09.482][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:09.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:09.486][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:09.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:09.496][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:09.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:09.504][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:09.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:09.520][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:09.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:09.535][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:09.536][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:09.538][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:09.560][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:09.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:09.564][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:09.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:09.570][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:09.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:09.577][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:09.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:09.594][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:09.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:09.610][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:09.612][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:09.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:09.633][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:09.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:09.636][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:09.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:09.648][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:09.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:09.665][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:09.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:09.704][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:09.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:09.720][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:09.721][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:09.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:09.744][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:09.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:09.748][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:09.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:09.758][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:09.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:09.765][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:09.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:09.781][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:09.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:09.798][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:09.800][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:09.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:09.822][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:09.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:09.826][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:09.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:09.836][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:09.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:09.859][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:09.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:09.874][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:09.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:09.882][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:09.889][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:09.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:09.920][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:09.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:09.924][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:09.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:09.935][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:09.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:09.951][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:09.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:09.969][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:09.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:09.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:09.982][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:09.984][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:09.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:10.018][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:10.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:10.023][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:10.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:10.036][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:10.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:10.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.049][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:10.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:10.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.066][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:10.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:10.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.114][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:10.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:10.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.159][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:10.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:10.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.190][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:10.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:10.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.207][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:10.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:10.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:10.224][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:10.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:10.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:10.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:10.310][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-29 19:22:10.315][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:22:10.316][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:22:10.327][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-05-29 19:22:10.668][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-05-29 19:22:11.010][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:22:11.013][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2024-05-29 19:22:11.020][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2024-05-29 19:22:11.025][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-29 19:22:11.030][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:22:11.031][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:22:11.034][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-05-29 19:22:11.375][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-05-29 19:22:11.715][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:22:11.718][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2024-05-29 19:22:11.724][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2024-05-29 19:22:11.729][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:11.731][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:11.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:11.740][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:11.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:11.743][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:11.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:11.746][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-05-29 19:22:11.747][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-29 19:22:11.750][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-05-29 19:22:11.751][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-29 19:22:11.753][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-29 19:22:11.754][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-29 19:22:11.756][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-29 19:22:11.757][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-29 19:22:11.759][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-29 19:22:11.762][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:11.764][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:11.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:11.792][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:11.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:11.795][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:11.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:11.798][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2024-05-29 19:22:11.802][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:22:11.803][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:22:11.805][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2024-05-29 19:22:12.149][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2024-05-29 19:22:12.495][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:22:12.499][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2024-05-29 19:22:12.505][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2024-05-29 19:22:12.510][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2024-05-29 19:22:12.513][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-29 19:22:12.515][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-29 19:22:12.517][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-29 19:22:12.519][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:12.521][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:12.522][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:12.531][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:12.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:12.534][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:12.535][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[2024-05-29 19:22:12.538][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:12.540][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:12.542][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.543][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:12.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:12.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.550][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:22:12.552][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:22:12.553][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.554][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.556][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:22:12.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:22:12.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.562][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:22:12.563][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:22:12.565][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.566][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.568][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:22:12.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:22:12.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.573][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:22:12.575][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:22:12.576][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.577][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.579][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:22:12.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:22:12.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.585][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:22:12.586][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:22:12.587][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.588][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.590][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:22:12.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:22:12.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.596][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:12.597][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:12.598][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.599][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.601][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:12.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:12.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.606][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:22:12.608][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:12.609][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.610][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.612][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:22:12.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:12.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.618][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:12.619][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:12.620][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.622][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.624][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:12.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:12.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.629][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:12.631][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:12.632][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.647][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.650][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:12.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:12.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.656][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:22:12.658][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:22:12.659][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.660][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.662][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:22:12.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:22:12.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.668][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:22:12.669][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:22:12.670][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.672][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.673][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:22:12.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:22:12.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.679][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:12.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:12.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.685][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:12.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:12.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:12.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:12.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.695][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:12.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:12.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:12.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:12.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:12.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:12.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:12.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:12.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:12.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:12.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:12.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:12.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:12.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:12.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:12.770][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-05-29 19:22:12.771][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:12.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:12.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.785][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:12.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:12.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.791][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:12.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:12.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:12.804][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:12.805][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:12.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:12.824][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:12.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:12.827][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:12.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:12.830][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:12.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:12.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.845][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:12.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:12.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:12.856][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:12.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:12.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:12.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:12.862][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:12.870][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:12.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:12.880][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:12.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:12.883][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:12.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:12.886][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-05-29 19:22:12.910][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-29 19:22:12.914][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-05-29 19:22:12.917][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-29 19:22:12.938][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-29 19:22:12.941][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-29 19:22:12.942][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-29 19:22:12.944][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-29 19:22:12.946][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-29 19:22:12.953][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:12.955][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:12.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:12.964][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:12.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:12.967][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:12.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:12.970][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2024-05-29 19:22:12.984][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:22:12.986][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:22:12.988][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2024-05-29 19:22:13.364][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2024-05-29 19:22:13.704][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:22:13.707][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2024-05-29 19:22:13.712][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2024-05-29 19:22:13.717][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2024-05-29 19:22:13.720][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-29 19:22:13.722][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-29 19:22:13.724][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-29 19:22:13.726][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:13.727][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:13.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:13.738][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:13.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:13.740][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:13.742][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.TRACE[2024-05-29 19:22:13.746][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:13.747][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:13.749][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:13.750][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:13.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:13.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:13.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:13.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:13.757][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:22:13.759][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:22:13.760][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:13.761][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:13.763][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:22:13.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:22:13.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:13.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:13.768][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:22:13.770][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:22:13.771][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:13.772][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:13.774][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:22:13.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:22:13.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:13.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:13.779][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:22:13.781][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:22:13.782][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:13.783][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:13.785][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:22:13.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:22:13.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:13.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:13.790][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:22:13.792][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:22:13.793][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:13.794][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:13.796][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:22:13.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:22:13.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:13.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:13.802][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:13.803][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:13.804][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:13.805][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:13.807][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:22:13.809][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:13.810][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:13.811][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:13.813][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:22:13.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:13.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:13.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:13.818][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:13.820][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:13.829][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:13.836][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:13.838][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:13.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:13.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:13.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:13.845][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:13.846][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:13.848][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:13.849][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:13.851][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:13.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:13.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:13.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:13.856][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:22:13.858][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:22:13.859][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:13.860][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:13.862][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:22:13.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:22:13.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:13.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:13.867][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:22:13.868][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:22:13.870][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:13.871][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:13.873][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:22:13.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:22:13.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:13.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:13.878][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:13.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:13.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:13.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:13.884][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:13.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:13.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:13.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:13.889][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:13.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:13.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:13.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:13.894][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:13.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:13.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:13.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:13.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:13.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:13.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:13.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:13.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:13.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:13.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:13.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:13.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:13.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:13.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:13.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:13.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:13.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:13.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:13.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:13.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:13.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:13.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:13.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:13.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:13.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:13.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:13.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:13.951][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-05-29 19:22:13.958][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:13.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:13.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:13.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:13.964][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:13.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:13.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:13.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:13.979][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:13.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:13.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:13.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:14.024][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-29 19:22:14.036][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-29 19:22:14.038][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-29 19:22:14.041][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-29 19:22:14.044][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-05-29 19:22:14.077][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:14.079][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:14.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:14.092][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:14.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:14.095][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:14.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:14.098][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:14.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:14.122][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:14.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:14.135][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:14.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:14.141][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:14.150][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:14.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:14.169][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:14.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:14.172][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:14.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:14.183][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:14.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:14.189][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:14.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:14.206][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:14.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:14.218][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:14.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:14.225][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:14.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:14.238][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:14.240][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:14.241][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:14.258][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:14.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:14.262][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:14.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:14.271][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:14.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:14.279][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:14.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:14.294][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:14.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:14.312][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:14.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:14.326][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:14.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:14.343][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:14.346][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:14.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:14.357][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:14.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:14.361][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:14.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:14.371][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:14.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:14.378][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:14.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:14.394][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:14.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:14.411][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:14.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:14.460][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:14.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:14.480][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:14.482][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:14.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:14.506][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:14.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:14.509][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:14.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:14.519][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:14.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:14.528][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:14.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:14.543][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:14.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:14.559][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:14.561][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:14.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:14.590][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:14.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:14.593][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:14.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:14.604][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:14.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:14.621][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:14.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:14.630][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:14.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:14.646][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:14.655][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:14.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:14.683][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:14.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:14.687][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:14.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:14.697][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:14.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:14.704][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:14.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:14.717][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:14.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:14.726][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:14.728][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:14.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:14.737][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:14.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:14.740][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:14.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:14.743][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:14.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:14.763][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:14.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:14.780][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:14.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:14.792][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:14.794][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:14.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:14.813][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:14.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:14.816][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:14.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:14.827][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:14.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:14.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:15.388][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:15.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:15.405][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:15.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:15.421][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:15.422][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:15.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:15.442][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:15.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:15.446][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:15.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:15.459][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:15.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:15.475][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:15.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:15.495][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:15.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:15.513][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:15.516][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:15.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:15.546][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:15.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:15.550][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:15.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:15.558][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:15.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:15.573][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:15.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:15.591][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:15.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:15.600][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:15.610][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:15.612][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:15.623][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:15.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:15.626][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:15.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:15.636][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:15.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:15.653][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:15.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:15.662][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:15.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:15.678][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:15.684][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:15.686][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:15.700][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:15.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:15.705][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:15.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:15.726][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:15.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:15.746][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:15.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:15.763][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:15.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:15.777][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:15.779][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:15.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:15.807][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:15.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:15.812][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:15.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:15.820][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:15.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:15.836][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:15.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:15.852][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:15.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:15.860][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:15.868][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:15.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:15.881][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:15.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:15.886][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:15.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:15.900][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:15.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:15.915][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:15.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:15.935][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:15.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:15.952][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:15.954][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:15.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:15.975][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:15.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:15.979][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:15.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:15.989][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:15.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:15.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:16.004][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:16.014][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:16.027][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:16.028][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:16.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:16.052][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:16.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:16.056][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:16.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:16.068][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:16.078][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:16.093][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:16.109][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:16.111][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:16.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:16.121][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:16.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:16.124][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:16.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:16.128][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:16.142][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:16.157][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:16.169][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:16.171][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:16.172][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:16.185][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:16.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:16.189][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:16.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:16.211][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:16.221][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:16.235][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:16.251][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:16.252][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:16.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:16.286][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:16.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:16.290][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:16.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:16.293][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:16.300][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:16.314][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:16.365][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-29 19:22:16.382][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-29 19:22:16.385][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-29 19:22:16.387][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-29 19:22:16.395][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-05-29 19:22:16.402][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:16.404][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:16.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:16.432][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:16.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:16.435][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:16.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:16.445][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:16.452][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:16.468][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:16.485][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:16.486][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:16.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:16.497][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:16.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:16.501][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:16.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:16.511][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:16.518][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:16.530][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:16.543][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:16.558][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:16.567][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:16.568][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:16.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:16.589][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:16.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:16.592][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:16.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:16.596][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:16.606][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:16.630][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:16.638][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:16.651][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:16.658][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:16.660][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:16.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:16.689][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:16.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:16.692][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:16.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:16.695][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:16.712][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:16.726][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:16.739][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:16.752][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:16.759][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:16.766][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:16.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:16.787][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:16.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:16.790][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:16.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:16.793][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:16.804][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:16.818][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:16.825][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:16.837][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:16.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:16.847][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:16.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:16.850][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:16.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:16.853][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:16.868][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:16.883][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:16.891][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:16.897][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:16.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:16.920][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:16.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:16.923][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:16.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:16.933][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:16.942][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:16.953][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:16.966][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:16.967][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:16.969][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:16.977][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:16.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:16.980][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:16.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:16.983][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:16.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:16.997][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:16.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:17.012][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:17.019][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:17.027][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:17.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:17.049][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:17.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:17.052][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:17.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:17.055][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:17.072][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:17.079][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:17.093][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:17.095][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:17.096][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:17.114][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:17.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:17.118][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:17.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:17.128][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:17.135][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:17.149][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:17.162][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:17.163][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:17.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:17.180][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:17.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:17.183][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:17.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:17.186][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:17.201][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:17.217][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:17.224][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:17.225][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:17.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:17.235][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:17.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:17.238][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:17.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:17.241][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:17.256][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:17.268][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:17.274][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:17.283][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:17.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:17.314][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:17.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:17.318][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:17.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:17.327][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:17.334][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:17.346][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:17.352][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:17.358][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:17.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:17.368][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:17.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:17.370][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:17.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:17.374][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:17.388][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:17.401][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:17.407][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:17.416][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:17.418][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:17.441][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:17.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:17.444][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:17.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:17.447][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:17.455][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:17.466][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:17.473][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:17.474][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:17.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:17.490][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:17.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:17.493][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:17.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:17.496][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:17.508][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:17.523][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:17.530][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:17.535][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:17.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:17.554][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:17.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:17.557][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:17.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:17.566][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:17.573][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:17.587][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:17.593][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:17.602][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:17.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:17.612][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:17.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:17.615][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:17.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:17.634][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:17.650][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:17.662][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:17.668][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:17.670][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:17.683][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:17.696][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:17.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:17.699][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:17.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:17.702][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:17.718][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:17.730][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:17.745][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:17.746][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:17.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:17.756][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:17.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:17.759][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:17.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:17.762][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:17.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:17.788][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:17.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:17.824][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-29 19:22:17.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-29 19:22:17.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-29 19:22:17.864][biodb::testThat]
biodb.INFO [2024-05-29 19:22:17.865][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-05-29 19:22:17.867][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:22:17.868][biodb::testThat]
biodb.TRACE[2024-05-29 19:22:17.880][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-29 19:22:17.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-29 19:22:17.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:17.887][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:17.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:17.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:17.902][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:17.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:17.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:17.930][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:17.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:17.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:17.945][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:17.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:17.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:17.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:17.958][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:17.960][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:17.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:17.969][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:17.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:17.973][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:17.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:17.988][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-29 19:22:17.994][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-29 19:22:18.004][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-05-29 19:22:18.007][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-29 19:22:18.010][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-05-29 19:22:18.023][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:18.024][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:18.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:18.047][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:18.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:18.050][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:18.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:18.060][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:18.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:18.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.069][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:18.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:18.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.083][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:18.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:18.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:18.103][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-29 19:22:18.116][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-29 19:22:18.121][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-05-29 19:22:18.124][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-29 19:22:18.132][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-05-29 19:22:18.137][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:18.139][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:18.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:18.176][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:18.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:18.180][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:18.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:18.193][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:18.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:18.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.205][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:18.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:18.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.212][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:18.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:18.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:18.222][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:18.224][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:18.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:18.240][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:18.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:18.244][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:18.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:18.254][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:18.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:18.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.262][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:18.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:18.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.277][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:18.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:18.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:18.299][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-29 19:22:18.302][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:18.304][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:18.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:18.325][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:18.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:18.328][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:18.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:18.340][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.348][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.362][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:18.364][private$selectFields]
biodb.TRACE[2024-05-29 19:22:18.371][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-29 19:22:18.373][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-29 19:22:18.375][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:18.377][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.378][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.386][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.388][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.390][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.392][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.394][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.404][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.408][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:18.410][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:18.412][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.414][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.423][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.425][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.427][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-29 19:22:18.429][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.442][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.456][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.498][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-05-29 19:22:18.508][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:18.510][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:18.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:18.536][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:18.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:18.541][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:18.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:18.553][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.565][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.572][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:18.577][private$selectFields]
biodb.TRACE[2024-05-29 19:22:18.579][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-29 19:22:18.580][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-29 19:22:18.582][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:18.584][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.585][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.595][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.597][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.598][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.600][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.602][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.611][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.615][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:18.617][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:18.619][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.622][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.629][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.631][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.633][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-29 19:22:18.634][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.649][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.665][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.677][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-05-29 19:22:18.680][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:18.681][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:18.683][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:18.705][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:18.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:18.709][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:18.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:18.721][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.737][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.753][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:18.755][private$selectFields]
biodb.TRACE[2024-05-29 19:22:18.756][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-29 19:22:18.758][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-29 19:22:18.786][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:18.789][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.791][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.800][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.802][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.804][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.806][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.808][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.814][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.817][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:18.818][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:18.821][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.822][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.832][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.835][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.837][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-29 19:22:18.840][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.858][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.874][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:18.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.889][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-05-29 19:22:18.891][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-29 19:22:18.894][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-29 19:22:18.933][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:18.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:18.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.951][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:18.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:18.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.967][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:18.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:18.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:18.981][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:18.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:18.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:18.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:19.157][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:19.167][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:19.169][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:19.180][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:19.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:19.185][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:19.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:19.200][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-29 19:22:19.221][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:22:19.224][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:22:19.236][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-05-29 19:22:19.613][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-05-29 19:22:20.163][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:22:20.166][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2024-05-29 19:22:20.173][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2024-05-29 19:22:20.178][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-29 19:22:20.183][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:22:20.185][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:22:20.187][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-05-29 19:22:20.806][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-05-29 19:22:21.164][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:22:21.168][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2024-05-29 19:22:21.174][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2024-05-29 19:22:21.178][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:21.180][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:21.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:21.190][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:21.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:21.193][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:21.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:21.196][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:21.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:21.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:21.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:21.202][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:21.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:21.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:21.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:21.208][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:21.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:21.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:21.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:21.214][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:21.215][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:21.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:21.225][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:21.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:21.228][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:21.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:21.231][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:21.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:21.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:21.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:21.237][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:21.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:21.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:21.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:21.242][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:21.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:21.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:21.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:21.248][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:21.249][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:21.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:21.259][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:21.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:21.262][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:21.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:21.265][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:21.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:21.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:21.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:21.271][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:21.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:21.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:21.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:21.277][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:21.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:21.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:21.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:21.318][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-29 19:22:21.353][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:21.354][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:21.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:21.367][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:21.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:21.370][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:21.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:21.374][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:21.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:21.386][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:21.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:21.401][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:21.402][private$selectFields]
biodb.TRACE[2024-05-29 19:22:21.405][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-29 19:22:21.406][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-29 19:22:21.413][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:21.415][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.417][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.419][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:21.421][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:21.422][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.430][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.432][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:21.434][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:21.435][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:21.437][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:21.438][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.447][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.449][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:21.451][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:21.453][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-29 19:22:21.454][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:21.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:21.493][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:21.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:21.508][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:21.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:21.518][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-05-29 19:22:21.526][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:21.528][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:21.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:21.548][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:21.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:21.551][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:21.552][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.TRACE[2024-05-29 19:22:21.590][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:21.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:21.603][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:21.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:21.672][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:21.675][private$selectFields]
biodb.TRACE[2024-05-29 19:22:21.677][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-29 19:22:21.678][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-29 19:22:21.680][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:21.681][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.691][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.692][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:21.694][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:21.695][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.697][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.698][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:21.704][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:21.706][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:21.731][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:21.739][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.741][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.743][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:21.744][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:21.746][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-29 19:22:21.747][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:21.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:21.759][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:21.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:21.774][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:21.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:21.781][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-05-29 19:22:21.786][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:21.787][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:21.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:21.807][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:21.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:21.811][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:21.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:21.814][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:21.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:21.822][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:21.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:21.837][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:21.838][private$selectFields]
biodb.TRACE[2024-05-29 19:22:21.840][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-29 19:22:21.841][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-29 19:22:21.843][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:21.844][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.847][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.848][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:21.850][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:21.851][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.852][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.854][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:21.855][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:21.864][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:21.866][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:21.867][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.869][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.870][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:21.872][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:21.880][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-29 19:22:21.882][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:21.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:21.888][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:21.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:21.899][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:21.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:21.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:21.912][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-05-29 19:22:21.913][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-29 19:22:21.915][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-29 19:22:21.935][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-29 19:22:21.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-29 19:22:21.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:21.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-29 19:22:21.947][biodb::testThat]
biodb.INFO [2024-05-29 19:22:21.949][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-05-29 19:22:21.950][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:22:21.952][biodb::testThat]
biodb.TRACE[2024-05-29 19:22:21.967][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-29 19:22:21.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-29 19:22:21.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:21.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:21.974][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:21.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:21.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:21.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:21.987][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:21.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:21.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:21.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:21.999][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:22.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:22.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:22.007][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:22.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:22.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:22.023][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:22.024][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:22.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:22.048][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:22.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:22.051][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:22.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:22.062][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-29 19:22:22.067][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-29 19:22:22.069][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-05-29 19:22:22.074][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-29 19:22:22.076][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-05-29 19:22:22.080][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:22.081][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:22.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:22.100][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:22.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:22.103][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:22.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:22.106][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:22.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:22.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:22.116][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:22.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:22.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:22.124][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:22.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:22.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:22.131][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-29 19:22:22.138][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-29 19:22:22.140][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-05-29 19:22:22.142][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-29 19:22:22.145][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-05-29 19:22:22.153][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:22.154][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:22.156][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:22.169][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:22.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:22.172][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:22.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:22.175][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:22.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:22.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:22.183][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:22.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:22.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:22.193][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:22.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:22.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:22.199][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:22.200][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:22.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:22.213][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:22.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:22.216][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:22.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:22.218][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:22.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:22.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:22.227][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:22.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:22.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:22.233][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:22.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:22.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:22.238][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-29 19:22:22.241][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:22.242][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:22.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:22.251][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:22.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:22.253][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:22.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:22.255][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:22.260][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:22.265][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:22.265][private$selectFields]
biodb.TRACE[2024-05-29 19:22:22.267][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-29 19:22:22.267][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-29 19:22:22.268][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:22.269][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.270][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.271][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.272][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:22.273][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.275][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.276][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.283][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:22.284][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:22.284][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:22.285][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.286][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.287][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.288][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:22.289][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-29 19:22:22.290][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:22.293][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:22.297][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:22.302][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-05-29 19:22:22.303][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:22.304][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:22.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:22.311][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:22.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:22.313][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:22.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:22.315][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:22.319][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:22.323][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:22.325][private$selectFields]
biodb.TRACE[2024-05-29 19:22:22.325][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-29 19:22:22.326][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-29 19:22:22.327][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:22.328][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.329][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.330][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.331][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:22.331][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.333][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.334][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.335][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:22.336][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:22.337][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:22.338][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.340][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.341][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.342][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:22.344][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-29 19:22:22.345][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:22.351][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:22.356][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:22.361][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-05-29 19:22:22.362][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:22.363][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:22.364][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:22.371][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:22.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:22.373][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:22.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:22.376][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:22.381][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:22.386][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:22.387][private$selectFields]
biodb.TRACE[2024-05-29 19:22:22.388][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-29 19:22:22.390][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-29 19:22:22.391][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:22.393][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.395][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.396][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.397][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:22.398][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.400][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.401][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.402][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:22.403][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:22.404][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:22.405][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.406][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.407][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.408][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:22.409][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-29 19:22:22.410][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:22.415][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:22.420][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:22.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:22.425][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-05-29 19:22:22.426][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-29 19:22:22.427][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-29 19:22:22.439][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:22.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:22.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:22.443][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:22.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:22.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:22.448][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:22.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:22.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:22.453][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:22.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:22.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:22.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:22.461][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:22.462][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:22.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:22.473][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:22.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:22.475][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:22.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:22.480][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-29 19:22:22.484][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:22:22.485][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:22:22.487][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-05-29 19:22:22.831][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-05-29 19:22:23.169][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2024-05-29 19:22:23.173][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-05-29 19:22:23.177][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2024-05-29 19:22:23.183][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2024-05-29 19:22:23.189][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-29 19:22:23.195][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:22:23.197][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:22:23.200][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-05-29 19:22:23.544][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-05-29 19:22:23.885][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:22:23.888][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2024-05-29 19:22:23.895][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2024-05-29 19:22:23.899][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:23.901][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:23.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:23.910][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:23.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:23.914][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:23.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:23.917][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:23.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:23.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:23.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:23.923][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:23.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:23.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:23.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:23.929][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:23.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:23.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:23.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:23.935][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:23.936][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:23.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:23.946][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:23.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:23.949][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:23.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:23.952][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:23.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:23.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:23.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:23.957][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:23.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:23.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:23.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:23.963][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:23.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:23.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:23.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:23.968][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:23.969][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:23.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:23.979][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:23.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:23.983][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:23.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:23.987][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:23.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:23.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:23.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:23.996][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:23.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:24.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:24.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:24.003][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:24.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:24.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:24.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:24.012][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-29 19:22:24.016][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:24.017][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:24.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:24.025][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:24.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:24.028][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:24.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:24.031][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:24.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:24.037][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:24.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:24.043][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:24.044][private$selectFields]
biodb.TRACE[2024-05-29 19:22:24.045][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-29 19:22:24.046][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-29 19:22:24.048][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:24.049][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.050][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.052][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:24.053][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:24.055][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.056][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.058][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:24.059][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:24.060][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:24.061][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:24.062][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.063][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.064][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:24.065][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:24.066][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-29 19:22:24.068][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:24.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:24.073][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:24.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:24.077][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:24.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:24.083][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-05-29 19:22:24.084][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:24.085][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:24.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:24.094][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:24.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:24.097][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:24.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:24.100][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:24.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:24.106][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:24.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:24.111][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:24.119][private$selectFields]
biodb.TRACE[2024-05-29 19:22:24.129][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-29 19:22:24.131][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-29 19:22:24.132][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:24.133][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.134][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.136][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:24.137][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:24.138][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.140][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.141][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:24.142][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:24.143][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:24.145][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:24.146][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.147][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.148][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:24.150][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:24.151][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-29 19:22:24.152][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:24.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:24.158][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:24.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:24.164][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:24.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:24.169][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-05-29 19:22:24.171][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:24.172][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:24.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:24.180][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:24.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:24.184][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:24.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:24.187][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:24.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:24.193][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:24.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:24.197][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:24.198][private$selectFields]
biodb.TRACE[2024-05-29 19:22:24.199][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-29 19:22:24.200][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-29 19:22:24.201][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:24.203][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.204][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.205][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:24.207][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:24.208][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.209][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.211][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:24.212][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:24.213][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:24.215][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:24.216][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.217][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.219][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:24.220][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:24.221][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-29 19:22:24.223][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:24.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:24.229][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:24.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:24.234][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:24.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:24.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:24.240][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-05-29 19:22:24.241][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-29 19:22:24.243][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-29 19:22:24.256][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-29 19:22:24.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-29 19:22:24.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:24.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-29 19:22:24.267][biodb::testThat]
biodb.INFO [2024-05-29 19:22:24.269][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-05-29 19:22:24.270][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:22:24.271][biodb::testThat]
biodb.TRACE[2024-05-29 19:22:24.276][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-29 19:22:24.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-29 19:22:24.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:24.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:24.282][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:24.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:24.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:24.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:24.287][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:24.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:24.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:24.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:24.293][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:24.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:24.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:24.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:24.299][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:24.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:24.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:24.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:24.311][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:24.313][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:24.314][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:24.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:24.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:24.325][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:24.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:24.331][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-29 19:22:24.335][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:22:24.337][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:22:24.340][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-05-29 19:22:24.682][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-05-29 19:22:25.030][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:22:25.034][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-05-29 19:22:25.043][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-05-29 19:22:25.052][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:25.053][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:25.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:25.067][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:25.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:25.071][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:25.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:25.075][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:25.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:25.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:25.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:25.102][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:25.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:25.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:25.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:25.110][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:25.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:25.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:25.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:25.117][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-29 19:22:25.122][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:22:25.123][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:22:25.127][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-05-29 19:22:25.492][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-05-29 19:22:25.834][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:22:25.837][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-05-29 19:22:25.843][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-05-29 19:22:25.847][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:25.849][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:25.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:25.858][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:25.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:25.861][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:25.862][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.TRACE[2024-05-29 19:22:25.864][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:25.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:25.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:25.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:25.870][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:25.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:25.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:25.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:25.875][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:25.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:25.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:25.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:25.880][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:25.881][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:25.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:25.890][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:25.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:25.893][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:25.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:25.896][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:25.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:25.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:25.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:25.901][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:25.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:25.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:25.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:25.907][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:25.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:25.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:25.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:25.912][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-29 19:22:25.914][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:25.916][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:25.917][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:25.924][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:25.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:25.927][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:25.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:25.930][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:25.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:25.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:25.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:25.935][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:25.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:25.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:25.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:25.941][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:25.942][private$selectFields]
biodb.TRACE[2024-05-29 19:22:25.944][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-29 19:22:25.945][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-29 19:22:25.946][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:25.948][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:25.949][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:25.950][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:25.951][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:25.953][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:25.954][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:25.956][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:25.957][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:25.958][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:25.960][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:25.961][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:25.963][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:25.964][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:25.965][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:25.966][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-29 19:22:25.968][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:25.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:25.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:25.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:25.973][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:25.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:25.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:25.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:25.979][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:25.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:25.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:25.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:25.984][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-05-29 19:22:25.986][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:25.987][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:25.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:25.996][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:25.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:25.999][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:26.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:26.002][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.008][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.018][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:26.020][private$selectFields]
biodb.TRACE[2024-05-29 19:22:26.021][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-29 19:22:26.023][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-29 19:22:26.024][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:26.025][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.027][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.030][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.033][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.034][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.036][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.037][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.038][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.039][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:26.044][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:26.046][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.047][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.049][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.050][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.051][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-29 19:22:26.061][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.068][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.113][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.132][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-05-29 19:22:26.135][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:26.137][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:26.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:26.169][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:26.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:26.173][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:26.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:26.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.198][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.206][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:26.214][private$selectFields]
biodb.TRACE[2024-05-29 19:22:26.216][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-29 19:22:26.218][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-29 19:22:26.220][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:26.222][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.230][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.232][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.234][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.236][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.237][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.244][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.246][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.248][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:26.249][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:26.251][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.260][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.263][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.265][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.266][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-29 19:22:26.268][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.279][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.284][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.299][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-05-29 19:22:26.301][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-29 19:22:26.303][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-29 19:22:26.353][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:26.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:26.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.379][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:26.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:26.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.396][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:26.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:26.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.410][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:26.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:26.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:26.430][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:26.432][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:26.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:26.461][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:26.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:26.465][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:26.466][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.DEBUG[2024-05-29 19:22:26.477][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-29 19:22:26.482][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-29 19:22:26.490][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-05-29 19:22:26.492][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-29 19:22:26.494][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-05-29 19:22:26.508][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-29 19:22:26.513][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-29 19:22:26.515][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-05-29 19:22:26.524][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-29 19:22:26.530][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-05-29 19:22:26.534][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:26.536][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:26.537][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:26.549][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:26.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:26.553][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:26.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:26.556][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:26.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:26.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.563][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:26.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:26.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.574][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:26.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:26.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:26.580][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:26.582][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:26.599][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:26.608][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:26.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:26.610][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:26.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:26.613][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:26.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:26.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.620][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:26.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:26.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.626][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:26.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:26.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:26.632][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:26.633][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:26.635][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:26.643][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:26.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:26.646][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:26.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:26.648][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:26.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:26.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.653][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:26.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:26.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.658][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:26.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:26.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:26.664][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-29 19:22:26.666][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:26.668][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:26.669][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:26.678][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:26.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:26.680][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:26.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:26.683][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.690][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.694][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:26.695][private$selectFields]
biodb.TRACE[2024-05-29 19:22:26.697][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-29 19:22:26.698][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-29 19:22:26.702][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:26.704][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.705][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.707][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.708][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.710][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.711][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.713][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.715][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.716][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:26.718][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:26.719][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.720][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.721][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.722][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.723][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-29 19:22:26.725][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.731][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.736][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.741][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-05-29 19:22:26.742][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:26.742][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:26.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:26.754][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:26.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:26.757][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:26.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:26.760][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.766][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.770][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:26.771][private$selectFields]
biodb.TRACE[2024-05-29 19:22:26.773][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-29 19:22:26.774][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-29 19:22:26.775][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:26.777][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.778][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.779][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.780][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.782][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.783][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.784][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.786][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.787][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:26.791][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:26.792][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.794][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.795][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.796][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.797][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-29 19:22:26.799][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.805][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.810][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.816][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-05-29 19:22:26.818][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:26.819][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:26.824][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:26.832][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:26.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:26.835][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:26.837][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.TRACE[2024-05-29 19:22:26.838][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.843][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.847][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:26.847][private$selectFields]
biodb.TRACE[2024-05-29 19:22:26.848][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-29 19:22:26.849][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-29 19:22:26.855][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:26.859][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.861][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.863][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.864][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.874][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.876][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.879][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.881][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.883][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:26.884][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-29 19:22:26.892][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.894][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.896][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.897][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.899][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-29 19:22:26.906][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.937][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.952][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:26.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:26.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:26.965][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-05-29 19:22:26.967][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-29 19:22:26.968][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-29 19:22:27.011][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-29 19:22:27.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-29 19:22:27.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:27.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-29 19:22:27.051][biodb::testThat]
biodb.INFO [2024-05-29 19:22:27.053][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-05-29 19:22:27.054][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:22:27.055][biodb::testThat]
biodb.DEBUG[2024-05-29 19:22:27.058][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-05-29 19:22:27.064][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-29 19:22:27.066][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-05-29 19:22:27.068][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-29 19:22:27.069][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-29 19:22:27.071][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-29 19:22:27.072][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-29 19:22:27.081][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-29 19:22:27.083][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-29 19:22:27.086][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:27.088][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:27.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:27.109][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:27.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:27.112][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:27.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:27.115][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2024-05-29 19:22:27.127][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:22:27.128][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:22:27.131][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2024-05-29 19:22:27.483][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2024-05-29 19:22:27.823][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:22:27.827][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2024-05-29 19:22:27.832][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2024-05-29 19:22:27.836][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2024-05-29 19:22:27.838][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-29 19:22:27.840][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-29 19:22:27.841][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-29 19:22:27.843][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:27.844][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:27.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:27.853][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:27.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:27.856][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:27.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:27.860][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:27.861][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:27.862][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:27.864][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:27.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:27.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:27.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:27.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:27.870][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:22:27.872][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:22:27.873][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:27.874][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:27.876][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:22:27.877][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:22:27.879][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:27.880][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:27.882][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:22:27.883][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:22:27.885][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:27.886][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:27.887][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:22:27.889][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:22:27.890][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:27.891][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:27.893][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:27.894][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:27.895][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:27.897][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:27.898][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:22:27.900][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:27.901][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:27.902][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:27.904][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:27.905][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:27.906][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:27.908][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:27.909][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:27.911][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:27.912][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:27.913][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:27.915][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:22:27.917][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:22:27.918][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:27.919][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:27.921][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:22:27.922][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:22:27.923][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:27.925][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:27.926][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:27.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:27.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:27.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:27.932][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:27.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:27.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:27.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:27.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:27.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:27.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:27.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:27.942][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:27.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:27.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:27.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:27.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:27.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:27.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:27.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:27.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:27.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:27.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:27.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:27.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:27.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:27.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:27.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:27.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:27.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:27.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:27.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:27.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:27.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:27.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:27.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:27.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:27.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:27.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:27.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:27.980][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-05-29 19:22:27.981][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-05-29 19:22:27.995][biodb::testThat]
biodb.INFO [2024-05-29 19:22:27.996][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-05-29 19:22:27.998][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:22:27.999][biodb::testThat]
biodb.DEBUG[2024-05-29 19:22:28.013][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-05-29 19:22:28.015][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-05-29 19:22:28.017][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-05-29 19:22:28.020][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-05-29 19:22:28.021][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2024-05-29 19:22:28.023][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-29 19:22:28.025][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-29 19:22:28.026][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-29 19:22:28.028][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-29 19:22:28.029][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-29 19:22:28.035][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:28.037][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:28.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:28.053][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:28.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:28.056][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:28.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:28.059][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2024-05-29 19:22:28.068][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:22:28.070][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:22:28.072][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2024-05-29 19:22:28.437][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2024-05-29 19:22:28.781][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:22:28.786][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2024-05-29 19:22:28.794][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2024-05-29 19:22:28.797][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:28.799][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:28.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:28.812][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:28.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:28.816][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:28.818][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[2024-05-29 19:22:28.821][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2024-05-29 19:22:28.826][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:22:28.828][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:22:28.830][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2024-05-29 19:22:29.173][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2024-05-29 19:22:29.511][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2024-05-29 19:22:29.512][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-05-29 19:22:29.514][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2024-05-29 19:22:29.517][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2024-05-29 19:22:29.519][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:29.521][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:29.522][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:29.529][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:29.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:29.532][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:29.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:29.548][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2024-05-29 19:22:29.552][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:22:29.553][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:22:29.555][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2024-05-29 19:22:29.920][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2024-05-29 19:22:30.273][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:22:30.276][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2024-05-29 19:22:30.290][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2024-05-29 19:22:30.295][private$doSaveContentToFile] Saving to cache [3]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2024-05-29 19:22:30.299][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-29 19:22:30.301][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-05-29 19:22:30.303][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-05-29 19:22:30.306][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:30.307][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:30.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:30.315][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:30.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:30.318][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:30.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:30.322][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:30.323][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:30.325][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.326][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.327][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:30.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:30.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.333][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:22:30.335][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:22:30.336][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.337][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.339][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:22:30.341][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:22:30.342][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.345][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.359][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:22:30.361][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:22:30.363][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.364][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.365][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:22:30.366][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:22:30.366][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.367][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.368][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:30.370][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:30.371][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.401][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.402][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:22:30.403][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:30.404][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.405][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.406][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:30.407][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:30.408][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.409][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.410][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:30.411][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:30.412][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.413][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.414][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:22:30.416][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:22:30.417][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.418][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.420][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:22:30.421][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:22:30.423][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.424][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.426][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:30.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:30.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.431][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:30.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:30.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:30.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:30.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.442][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:30.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:30.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.445][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:30.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:30.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:30.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:30.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:30.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:30.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:30.459][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:30.460][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:30.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:30.473][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:30.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:30.476][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:30.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:30.482][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:30.484][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:30.485][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.487][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:30.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:30.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.522][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:22:30.524][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:22:30.526][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.527][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.535][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:22:30.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:22:30.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.541][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:22:30.542][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:22:30.543][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.546][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.549][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:22:30.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:22:30.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.554][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:22:30.555][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:22:30.556][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.557][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.559][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:22:30.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:22:30.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.566][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:22:30.567][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:22:30.568][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.569][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.570][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:22:30.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:22:30.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.575][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:30.587][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:30.588][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.590][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.592][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:30.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:30.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.596][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:22:30.609][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:30.611][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.612][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.614][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:22:30.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:30.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.619][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:30.620][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:30.621][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.623][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.624][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:30.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:30.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.631][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:30.632][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:30.633][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.634][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.636][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:30.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:30.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.644][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:22:30.645][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:22:30.647][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.648][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.650][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:22:30.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:22:30.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.658][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:22:30.659][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:22:30.661][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.662][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.666][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:22:30.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:22:30.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.671][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:30.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:30.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.675][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:30.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:30.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:30.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:30.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.688][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:30.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:30.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:30.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:30.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:30.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:30.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:30.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:30.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:30.720][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:30.721][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:30.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:30.738][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:30.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:30.745][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:30.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:30.758][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:30.759][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:30.761][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.762][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:30.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:30.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.821][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:22:30.830][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:22:30.832][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.834][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.836][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:22:30.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:22:30.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.851][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:22:30.852][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:22:30.854][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.855][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.857][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:22:30.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:22:30.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.873][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:22:30.875][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:22:30.886][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.888][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.890][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:22:30.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:22:30.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.908][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:22:30.910][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:22:30.911][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.912][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.915][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:22:30.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:22:30.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.926][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:30.928][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:30.929][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.930][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.942][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:30.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:30.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.949][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:22:30.950][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:30.959][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.960][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.962][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:22:30.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:30.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.979][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:30.981][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:30.983][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:30.984][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:30.986][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:30.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:30.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:31.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:31.002][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:31.004][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:31.005][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:31.006][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:31.018][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:31.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:31.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:31.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:31.025][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:22:31.033][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:22:31.035][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:31.037][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:31.039][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:22:31.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:22:31.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:31.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:31.052][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:22:31.053][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:22:31.055][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:31.056][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:31.066][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:22:31.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:22:31.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:31.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:31.074][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:31.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:31.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:31.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:31.088][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:31.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:31.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:31.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:31.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:31.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:31.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:31.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:31.111][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:31.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:31.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:31.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:31.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:31.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:31.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:31.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:31.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:31.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:31.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:31.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:31.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:31.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:31.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:31.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:31.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:31.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:31.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:31.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:31.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:31.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:31.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:31.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:31.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:31.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:31.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:31.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:31.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:31.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:31.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:31.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:31.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:31.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:31.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:31.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:31.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:31.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:31.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:31.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:31.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:31.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:31.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:31.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:31.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:31.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:31.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:31.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:31.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:31.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:31.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:31.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:31.282][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-05-29 19:22:31.284][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-29 19:22:31.285][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-05-29 19:22:31.322][biodb::testThat]
biodb.INFO [2024-05-29 19:22:31.324][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-05-29 19:22:31.325][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:22:31.327][biodb::testThat]
biodb.INFO [2024-05-29 19:22:31.385][biodb::testThat]
biodb.INFO [2024-05-29 19:22:31.387][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-05-29 19:22:31.389][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:22:31.390][biodb::testThat]
biodb.INFO [2024-05-29 19:22:31.403][biodb::testThat]
biodb.INFO [2024-05-29 19:22:31.405][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-05-29 19:22:31.406][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:22:31.408][biodb::testThat]
biodb.DEBUG[2024-05-29 19:22:31.411][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2024-05-29 19:22:31.446][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:22:31.448][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:22:31.450][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2024-05-29 19:22:38.021][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2024-05-29 19:22:38.529][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:22:38.531][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2024-05-29 19:22:38.535][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2024-05-29 19:22:38.547][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:38.548][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:38.549][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:38.550][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:38.551][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:38.551][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:38.552][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:38.553][ef$get] fields variable is a list.
biodb.INFO [2024-05-29 19:22:38.554][biodb::testThat]
biodb.INFO [2024-05-29 19:22:38.555][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-05-29 19:22:38.556][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:22:38.557][biodb::testThat]
biodb.ERROR[2024-05-29 19:22:38.570][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-05-29 19:22:38.620][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-05-29 19:22:38.636][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-29 19:22:38.637][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-05-29 19:22:38.638][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-05-29 19:22:38.639][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-29 19:22:38.640][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:38.641][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:38.642][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:38.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:38.643][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:38.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-29 19:22:38.655][biodb::testContext]
biodb.INFO [2024-05-29 19:22:38.656][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-29 19:22:38.657][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-05-29 19:22:38.657][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-29 19:22:38.658][biodb::testContext]
biodb.INFO [2024-05-29 19:22:38.660][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-29 19:22:38.662][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-29 19:22:38.666][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-29 19:22:38.667][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-29 19:22:38.668][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-29 19:22:38.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:38.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:38.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:38.671][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-29 19:22:38.672][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-29 19:22:38.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:38.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:38.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:38.697][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-29 19:22:38.697][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-29 19:22:38.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:38.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:38.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:38.701][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-29 19:22:38.701][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-29 19:22:38.702][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-29 19:22:38.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:38.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:38.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:38.706][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-29 19:22:38.707][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-29 19:22:38.708][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-29 19:22:38.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:38.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:38.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:38.712][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-29 19:22:38.713][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-29 19:22:38.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:38.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:38.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:38.716][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-29 19:22:38.716][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-29 19:22:38.717][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-29 19:22:38.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:38.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:38.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:38.721][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-29 19:22:38.722][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-29 19:22:38.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:38.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:38.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:38.726][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-29 19:22:38.727][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-29 19:22:38.728][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-29 19:22:38.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:38.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:38.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:38.732][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-29 19:22:38.732][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-29 19:22:38.733][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-29 19:22:38.734][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-29 19:22:38.735][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-29 19:22:38.736][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-29 19:22:38.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:38.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:38.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:38.739][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-29 19:22:38.741][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-29 19:22:38.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:38.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:38.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:38.744][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-29 19:22:38.745][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-29 19:22:38.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:38.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:38.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:38.748][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-29 19:22:38.748][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-29 19:22:38.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:38.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:38.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:38.751][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-29 19:22:38.752][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-29 19:22:38.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:38.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:38.754][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[2024-05-29 19:22:38.755][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-29 19:22:38.756][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-29 19:22:38.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:38.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:38.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:38.759][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-29 19:22:38.760][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-29 19:22:39.363][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-29 19:22:39.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:39.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:39.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:39.367][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-29 19:22:39.367][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-29 19:22:39.368][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-29 19:22:39.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:39.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:39.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:39.372][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-29 19:22:39.373][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:39.374][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-29 19:22:39.375][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:39.376][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-29 19:22:39.377][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:39.377][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-29 19:22:39.378][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:39.379][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-29 19:22:39.380][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-29 19:22:39.381][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-29 19:22:39.382][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:39.383][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-29 19:22:39.384][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-29 19:22:39.384][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:39.385][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:39.386][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-29 19:22:39.386][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-29 19:22:39.386][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-29 19:22:39.386][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-29 19:22:39.386][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-29 19:22:39.387][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-29 19:22:39.388][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:39.389][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:39.390][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-29 19:22:39.391][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:39.391][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:39.392][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-29 19:22:39.393][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:39.394][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-29 19:22:39.395][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-29 19:22:39.395][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:39.396][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:39.397][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-29 19:22:39.399][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:39.400][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-29 19:22:39.401][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:39.402][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-29 19:22:39.403][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:39.404][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-29 19:22:39.405][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:39.406][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-29 19:22:39.407][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-29 19:22:39.408][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-29 19:22:39.409][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:39.410][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-29 19:22:39.421][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-29 19:22:39.423][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:39.424][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:39.436][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-29 19:22:39.436][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-29 19:22:39.436][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-29 19:22:39.436][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-29 19:22:39.436][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-29 19:22:39.437][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-29 19:22:39.438][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:39.438][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:39.439][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-29 19:22:39.440][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:39.441][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:39.442][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-29 19:22:39.443][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:39.444][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-29 19:22:39.444][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-29 19:22:39.456][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:39.457][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:39.458][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-29 19:22:39.470][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:39.471][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-29 19:22:39.472][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:39.479][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-29 19:22:39.485][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:39.486][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-29 19:22:39.487][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:39.488][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-29 19:22:39.489][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-29 19:22:39.490][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-29 19:22:39.491][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:39.492][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-29 19:22:39.492][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-29 19:22:39.493][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:39.494][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:39.495][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:39.506][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-29 19:22:39.506][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:39.507][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:39.508][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-29 19:22:39.508][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:39.509][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:39.510][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-29 19:22:39.511][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:39.512][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-29 19:22:39.513][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-29 19:22:39.514][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:39.514][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:39.515][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-29 19:22:39.517][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:39.518][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-29 19:22:39.518][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:39.519][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-29 19:22:39.520][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:39.521][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-29 19:22:39.522][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:39.522][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-29 19:22:39.523][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-29 19:22:39.537][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-29 19:22:39.537][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:39.538][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-29 19:22:39.539][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-29 19:22:39.540][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:39.541][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:39.551][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:39.552][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-29 19:22:39.553][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:39.554][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:39.555][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-29 19:22:39.556][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:39.556][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:39.557][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-29 19:22:39.558][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:39.558][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-29 19:22:39.559][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-29 19:22:39.560][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:39.561][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:39.562][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-29 19:22:39.562][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:39.563][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[2024-05-29 19:22:39.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:39.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:39.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:39.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:39.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:39.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:39.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:39.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:39.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:39.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:39.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:39.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:39.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:39.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:39.585][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[2024-05-29 19:22:39.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:39.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:39.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:39.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:39.588][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[2024-05-29 19:22:39.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:39.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:39.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:39.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:39.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:39.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:39.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:39.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:39.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:39.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:39.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:39.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:39.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:39.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:39.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:39.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:39.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:39.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:39.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:39.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:39.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:39.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:39.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:39.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:39.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:39.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:39.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:39.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:39.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:39.620][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[2024-05-29 19:22:39.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:39.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:39.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:39.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:39.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:39.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:39.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:39.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:39.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:39.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:39.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:39.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:39.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:39.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:39.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:39.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:39.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:39.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:39.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:39.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:39.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:39.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:39.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:39.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:39.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:39.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:39.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:39.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:39.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:39.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:39.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:39.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:39.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:39.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:39.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:39.667][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-29 19:22:39.669][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-29 19:22:39.670][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-29 19:22:39.671][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-29 19:22:39.672][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-29 19:22:39.673][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-29 19:22:39.674][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-29 19:22:39.675][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-29 19:22:39.677][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-29 19:22:39.678][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-29 19:22:39.679][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-29 19:22:39.680][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-29 19:22:39.681][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-29 19:22:39.682][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-29 19:22:39.683][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-29 19:22:39.684][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-29 19:22:39.698][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-29 19:22:39.699][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-29 19:22:39.701][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-29 19:22:39.702][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-29 19:22:39.703][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-29 19:22:39.704][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-29 19:22:39.705][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-29 19:22:39.707][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-29 19:22:39.708][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-29 19:22:39.709][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-29 19:22:39.710][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-29 19:22:39.712][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-29 19:22:39.713][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-29 19:22:39.714][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-29 19:22:39.716][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-29 19:22:39.717][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-29 19:22:39.718][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-29 19:22:39.719][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-29 19:22:39.721][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-29 19:22:39.722][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-29 19:22:39.723][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-29 19:22:39.724][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-29 19:22:39.738][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-29 19:22:39.739][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-29 19:22:39.740][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-29 19:22:39.741][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-29 19:22:39.742][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-29 19:22:39.744][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-29 19:22:39.745][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-29 19:22:39.746][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-29 19:22:39.747][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-29 19:22:39.748][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-29 19:22:39.749][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-29 19:22:39.750][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-29 19:22:39.752][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-29 19:22:39.754][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-29 19:22:39.755][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-29 19:22:39.756][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-29 19:22:39.758][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-29 19:22:39.759][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-29 19:22:39.760][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-29 19:22:39.761][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-29 19:22:39.762][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-29 19:22:39.763][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-29 19:22:39.764][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-29 19:22:39.766][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-29 19:22:39.767][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-29 19:22:39.768][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-29 19:22:39.769][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-29 19:22:39.770][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-29 19:22:39.771][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-29 19:22:39.772][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-29 19:22:39.774][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-29 19:22:39.775][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-29 19:22:39.776][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-29 19:22:39.777][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-29 19:22:39.778][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-29 19:22:39.779][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-29 19:22:39.781][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-29 19:22:39.782][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-29 19:22:39.783][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-29 19:22:39.784][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-29 19:22:39.785][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-29 19:22:39.786][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-29 19:22:39.787][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-29 19:22:39.799][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-29 19:22:39.800][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-29 19:22:39.801][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-29 19:22:39.803][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-29 19:22:39.803][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-29 19:22:39.804][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:39.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:39.805][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:39.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:39.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:39.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:39.808][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:39.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:39.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:39.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:39.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:39.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:39.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:39.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:39.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:39.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:39.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:39.837][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[2024-05-29 19:22:39.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:39.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:39.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:39.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:39.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:39.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:39.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:39.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:39.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:39.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:39.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:39.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:39.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:39.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:39.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:39.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:39.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:39.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:39.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:39.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:39.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:39.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:39.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:39.856][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:39.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:39.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:39.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:39.859][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[2024-05-29 19:22:39.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:39.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:39.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:39.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:39.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:39.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:39.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:39.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:39.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:39.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:39.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:39.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:39.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:39.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:39.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:39.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:39.872][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:39.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:39.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:39.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:39.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:39.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:39.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:39.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:39.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:39.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:39.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:39.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:39.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:39.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:39.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:39.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:39.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:39.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:39.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:39.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:39.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:39.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:39.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:39.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:39.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:39.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:39.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:39.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:39.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:40.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:40.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:40.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:40.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:40.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:40.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:40.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:40.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:40.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:40.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:40.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:40.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:40.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:40.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:40.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:40.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:40.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:40.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:40.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:40.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:40.015][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:40.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:40.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:40.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:40.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:40.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:40.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:40.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:40.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:40.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:40.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:40.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:40.026][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-05-29 19:22:40.028][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-05-29 19:22:40.029][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:40.030][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-29 19:22:40.031][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:40.032][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-29 19:22:40.033][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:40.033][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-29 19:22:40.034][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:40.035][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-05-29 19:22:40.036][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-29 19:22:40.036][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-29 19:22:40.037][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:40.038][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-05-29 19:22:40.039][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-29 19:22:40.039][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-05-29 19:22:40.039][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-05-29 19:22:40.039][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-05-29 19:22:40.039][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-05-29 19:22:40.039][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-05-29 19:22:40.039][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-05-29 19:22:40.039][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-05-29 19:22:40.039][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-05-29 19:22:40.039][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-05-29 19:22:40.039][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-05-29 19:22:40.039][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-05-29 19:22:40.041][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:40.041][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-29 19:22:40.041][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-29 19:22:40.041][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-29 19:22:40.043][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-29 19:22:40.044][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:40.045][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:40.046][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-29 19:22:40.046][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:40.047][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:40.048][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-29 19:22:40.048][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-29 19:22:40.048][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-05-29 19:22:40.049][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-29 19:22:40.050][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-29 19:22:40.051][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:40.051][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-05-29 19:22:40.051][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-05-29 19:22:40.052][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-29 19:22:40.054][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-29 19:22:40.056][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-05-29 19:22:40.057][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-29 19:22:40.058][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-29 19:22:40.059][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-29 19:22:40.062][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-05-29 19:22:40.063][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-05-29 19:22:40.064][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-05-29 19:22:40.065][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-05-29 19:22:40.066][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-29 19:22:40.067][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-29 19:22:40.070][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-05-29 19:22:40.071][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-05-29 19:22:40.072][biodb::testThat]
biodb.INFO [2024-05-29 19:22:40.073][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2024-05-29 19:22:40.073][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:22:40.074][biodb::testThat]
biodb.DEBUG[2024-05-29 19:22:40.078][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-05-29 19:22:40.082][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:22:40.083][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:22:40.084][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2024-05-29 19:22:40.426][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2024-05-29 19:22:40.917][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:22:40.920][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2024-05-29 19:22:40.938][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2024-05-29 19:22:40.954][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-29 19:22:40.959][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:22:40.961][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:22:40.964][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-05-29 19:22:41.308][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-05-29 19:22:41.649][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:22:41.652][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2024-05-29 19:22:41.658][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2024-05-29 19:22:41.661][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:41.663][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:41.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:41.672][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:41.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:41.675][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:41.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:41.679][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-29 19:22:41.684][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:22:41.685][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:22:41.687][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-05-29 19:22:42.031][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-05-29 19:22:42.372][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:22:42.375][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2024-05-29 19:22:42.382][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2024-05-29 19:22:42.386][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:42.387][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:42.388][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:42.396][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:42.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:42.399][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:42.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:42.433][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:42.434][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:42.436][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:42.444][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:42.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:42.448][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:42.449][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[2024-05-29 19:22:42.458][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-29 19:22:42.465][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-29 19:22:42.467][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-05-29 19:22:42.469][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-29 19:22:42.471][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-05-29 19:22:42.475][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:42.477][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:42.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:42.491][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:42.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:42.494][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:42.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:42.501][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-29 19:22:42.506][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-29 19:22:42.509][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-05-29 19:22:42.511][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-29 19:22:42.514][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-05-29 19:22:42.516][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:42.518][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:42.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:42.528][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:42.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:42.541][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:42.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:42.545][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:42.547][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:42.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:42.557][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:42.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:42.560][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:42.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:42.567][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-29 19:22:42.572][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-29 19:22:42.574][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-05-29 19:22:42.577][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-29 19:22:42.579][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-05-29 19:22:42.582][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:42.583][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:42.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:42.594][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:42.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:42.597][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:42.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:42.619][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-29 19:22:42.626][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-29 19:22:42.629][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-05-29 19:22:42.631][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-29 19:22:42.635][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-05-29 19:22:42.638][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:42.640][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:42.641][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:42.665][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:42.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:42.668][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:42.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:42.674][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-29 19:22:42.680][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:22:42.682][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:22:42.686][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-05-29 19:22:43.044][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-05-29 19:22:43.411][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:22:43.415][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2024-05-29 19:22:43.431][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2024-05-29 19:22:43.436][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:43.442][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:43.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:43.463][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:43.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:43.466][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:43.468][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.INFO [2024-05-29 19:22:43.503][biodb::testThat]
biodb.INFO [2024-05-29 19:22:43.506][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2024-05-29 19:22:43.511][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:22:43.513][biodb::testThat]
biodb.DEBUG[2024-05-29 19:22:43.520][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-29 19:22:43.534][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:22:43.536][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:22:43.556][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-05-29 19:22:43.944][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-05-29 19:22:44.291][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:22:44.295][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2024-05-29 19:22:44.300][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2024-05-29 19:22:44.303][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:44.304][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:44.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:44.312][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:44.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:44.313][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:44.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:44.319][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-29 19:22:44.323][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:22:44.324][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:22:44.327][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-05-29 19:22:44.697][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-05-29 19:22:45.037][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:22:45.039][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2024-05-29 19:22:45.043][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2024-05-29 19:22:45.045][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:45.046][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:45.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:45.053][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:45.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:45.054][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:45.055][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.INFO [2024-05-29 19:22:45.060][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-29 19:22:45.062][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-05-29 19:22:45.063][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-05-29 19:22:45.064][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-29 19:22:45.064][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:45.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:45.066][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:45.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:45.067][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:45.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-29 19:22:45.075][biodb::testContext]
biodb.INFO [2024-05-29 19:22:45.076][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-29 19:22:45.076][biodb::testContext] Test context - Test web services
biodb.INFO [2024-05-29 19:22:45.077][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-29 19:22:45.078][biodb::testContext]
biodb.INFO [2024-05-29 19:22:45.080][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-29 19:22:45.082][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-29 19:22:45.085][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-29 19:22:45.088][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-29 19:22:45.090][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-29 19:22:45.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:45.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:45.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:45.093][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-29 19:22:45.094][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-29 19:22:45.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:45.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:45.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:45.097][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-29 19:22:45.098][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-29 19:22:45.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:45.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:45.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:45.101][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-29 19:22:45.102][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-29 19:22:45.103][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-29 19:22:45.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:45.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:45.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:45.116][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-29 19:22:45.117][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-29 19:22:45.118][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-29 19:22:45.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:45.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:45.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:45.121][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-29 19:22:45.122][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-29 19:22:45.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:45.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:45.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:45.125][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-29 19:22:45.126][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-29 19:22:45.137][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-29 19:22:45.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:45.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:45.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:45.140][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-29 19:22:45.141][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-29 19:22:45.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:45.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:45.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:45.144][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-29 19:22:45.145][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-29 19:22:45.145][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-29 19:22:45.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:45.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:45.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:45.148][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-29 19:22:45.149][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-29 19:22:45.150][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-29 19:22:45.151][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-29 19:22:45.152][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-29 19:22:45.152][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-29 19:22:45.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:45.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:45.155][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[2024-05-29 19:22:45.156][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-29 19:22:45.157][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-29 19:22:45.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:45.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:45.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:45.160][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-29 19:22:45.161][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-29 19:22:45.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:45.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:45.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:45.164][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-29 19:22:45.165][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-29 19:22:45.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:45.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:45.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:45.168][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-29 19:22:45.169][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-29 19:22:45.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:45.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:45.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:45.172][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-29 19:22:45.183][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-29 19:22:45.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:45.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:45.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:45.186][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-29 19:22:45.187][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-29 19:22:45.888][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-29 19:22:45.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:45.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:45.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:45.891][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-29 19:22:45.892][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-29 19:22:45.893][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-29 19:22:45.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:45.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:45.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:45.908][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-29 19:22:45.910][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:45.912][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-29 19:22:45.913][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:45.914][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-29 19:22:45.914][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:45.915][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-29 19:22:45.916][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:45.917][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-29 19:22:45.918][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-29 19:22:45.919][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-29 19:22:45.920][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:45.921][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-29 19:22:45.922][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-29 19:22:45.923][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:45.925][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:45.925][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-29 19:22:45.925][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-29 19:22:45.925][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-29 19:22:45.925][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-29 19:22:45.925][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-29 19:22:45.926][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-29 19:22:45.927][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:45.928][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:45.929][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-29 19:22:45.930][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:45.932][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:45.933][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-29 19:22:45.933][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:45.934][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-29 19:22:45.935][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-29 19:22:45.936][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:45.937][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:45.938][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-29 19:22:45.939][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:45.940][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-29 19:22:45.941][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:45.942][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-29 19:22:45.944][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:45.944][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-29 19:22:45.945][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:45.946][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-29 19:22:45.947][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-29 19:22:45.948][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-29 19:22:45.949][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:45.951][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-29 19:22:45.952][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-29 19:22:45.954][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:45.955][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:45.956][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-29 19:22:45.956][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-29 19:22:45.956][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-29 19:22:45.956][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-29 19:22:45.956][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-29 19:22:45.957][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-29 19:22:45.957][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:45.958][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:45.959][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-29 19:22:45.960][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:45.961][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:45.963][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-29 19:22:45.964][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:45.964][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-29 19:22:45.965][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-29 19:22:45.966][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:45.967][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:45.969][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-29 19:22:45.971][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:45.972][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-29 19:22:45.984][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:45.988][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-29 19:22:45.989][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:45.991][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-29 19:22:45.992][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:45.993][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-29 19:22:45.995][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-29 19:22:45.996][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-29 19:22:45.997][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:45.998][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-29 19:22:45.999][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-29 19:22:46.000][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:46.001][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:46.002][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:46.003][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-29 19:22:46.003][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:46.004][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:46.005][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-29 19:22:46.006][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:46.006][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:46.024][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-29 19:22:46.025][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:46.026][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-29 19:22:46.027][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-29 19:22:46.028][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:46.029][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:46.030][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-29 19:22:46.032][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:46.032][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-29 19:22:46.033][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:46.035][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-29 19:22:46.036][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:46.037][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-29 19:22:46.039][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:46.040][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-29 19:22:46.040][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-29 19:22:46.041][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-29 19:22:46.042][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:46.043][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-29 19:22:46.044][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-29 19:22:46.045][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:46.047][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:46.048][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:46.048][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-29 19:22:46.049][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:46.050][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:46.051][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-29 19:22:46.052][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:46.053][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:46.054][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-29 19:22:46.055][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:46.056][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-29 19:22:46.057][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-29 19:22:46.058][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:46.059][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:46.073][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-29 19:22:46.074][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:46.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:46.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:46.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:46.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:46.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:46.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:46.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:46.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:46.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:46.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:46.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:46.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:46.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:46.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:46.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:46.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:46.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:46.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:46.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:46.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:46.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:46.107][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:46.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:46.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:46.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:46.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:46.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:46.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:46.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:46.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:46.122][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[2024-05-29 19:22:46.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:46.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:46.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:46.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:46.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:46.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:46.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:46.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:46.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:46.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:46.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:46.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:46.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:46.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:46.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:46.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:46.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:46.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:46.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:46.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:46.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:46.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:46.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:46.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:46.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:46.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:46.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:46.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:46.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:46.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:46.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:46.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:46.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:46.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:46.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:46.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:46.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:46.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:46.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:46.189][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[2024-05-29 19:22:46.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:46.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:46.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:46.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:46.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:46.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:46.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:46.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:46.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:46.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:46.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:46.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:46.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:46.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:46.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:46.210][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-29 19:22:46.211][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-29 19:22:46.217][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-29 19:22:46.219][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-29 19:22:46.220][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-29 19:22:46.221][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-29 19:22:46.223][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-29 19:22:46.225][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-29 19:22:46.226][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-29 19:22:46.229][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-29 19:22:46.231][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-29 19:22:46.232][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-29 19:22:46.234][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-29 19:22:46.235][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-29 19:22:46.237][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-29 19:22:46.240][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-29 19:22:46.242][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-29 19:22:46.244][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-29 19:22:46.245][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-29 19:22:46.246][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-29 19:22:46.248][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-29 19:22:46.249][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-29 19:22:46.250][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-29 19:22:46.252][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-29 19:22:46.254][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-29 19:22:46.256][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-29 19:22:46.257][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-29 19:22:46.259][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-29 19:22:46.260][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-29 19:22:46.262][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-29 19:22:46.265][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-29 19:22:46.267][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-29 19:22:46.269][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-29 19:22:46.270][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-29 19:22:46.272][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-29 19:22:46.274][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-29 19:22:46.276][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-29 19:22:46.278][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-29 19:22:46.280][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-29 19:22:46.286][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-29 19:22:46.288][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-29 19:22:46.291][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-29 19:22:46.293][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-29 19:22:46.298][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-29 19:22:46.301][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-29 19:22:46.304][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-29 19:22:46.307][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-29 19:22:46.312][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-29 19:22:46.318][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-29 19:22:46.321][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-29 19:22:46.323][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-29 19:22:46.327][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-29 19:22:46.329][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-29 19:22:46.331][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-29 19:22:46.341][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-29 19:22:46.343][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-29 19:22:46.349][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-29 19:22:46.355][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-29 19:22:46.360][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-29 19:22:46.395][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-29 19:22:46.397][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-29 19:22:46.399][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-29 19:22:46.402][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-29 19:22:46.416][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-29 19:22:46.419][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-29 19:22:46.421][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-29 19:22:46.424][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-29 19:22:46.429][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-29 19:22:46.432][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-29 19:22:46.434][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-29 19:22:46.436][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-29 19:22:46.438][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-29 19:22:46.440][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-29 19:22:46.443][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-29 19:22:46.445][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-29 19:22:46.450][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-29 19:22:46.453][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-29 19:22:46.455][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-29 19:22:46.458][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-29 19:22:46.460][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-29 19:22:46.467][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-29 19:22:46.469][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-29 19:22:46.472][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-29 19:22:46.474][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-29 19:22:46.483][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-29 19:22:46.485][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-29 19:22:46.487][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:46.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:46.490][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:46.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:46.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:46.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:46.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:46.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:46.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:46.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:46.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:46.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:46.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:46.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:46.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:46.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:46.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:46.507][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[2024-05-29 19:22:46.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:46.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:46.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:46.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:46.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:46.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:46.516][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[2024-05-29 19:22:46.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:46.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:46.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:46.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:46.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:46.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:46.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:46.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:46.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:46.529][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:46.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:46.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:46.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:46.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:46.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:46.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:46.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:46.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:46.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:46.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:46.538][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[2024-05-29 19:22:46.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:46.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:46.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:46.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:46.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:46.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:46.551][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[2024-05-29 19:22:46.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:46.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:46.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:46.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:46.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:46.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:46.558][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[2024-05-29 19:22:46.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:46.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:46.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:46.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:46.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:46.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:46.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:46.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:46.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:46.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:46.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:46.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:46.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:46.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:46.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:46.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:46.577][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:46.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:46.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:46.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:46.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:46.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:46.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:46.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:46.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:46.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:46.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:46.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:46.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:46.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:46.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:46.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:46.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:46.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:46.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:46.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:46.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:46.596][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:46.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:46.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:46.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:46.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:46.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:46.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:46.615][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:46.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:46.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:46.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:46.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:46.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:46.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:46.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:46.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:46.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:46.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:46.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:46.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:46.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:46.633][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:46.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:46.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:46.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:46.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:46.641][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-05-29 19:22:46.644][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-05-29 19:22:46.646][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:46.647][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-29 19:22:46.649][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:46.651][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-29 19:22:46.652][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:46.653][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-29 19:22:46.655][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:46.656][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-05-29 19:22:46.657][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-29 19:22:46.658][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-29 19:22:46.659][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:46.661][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-05-29 19:22:46.662][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-29 19:22:46.663][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-05-29 19:22:46.663][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-05-29 19:22:46.663][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-05-29 19:22:46.663][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-05-29 19:22:46.663][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-05-29 19:22:46.663][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-05-29 19:22:46.663][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-05-29 19:22:46.663][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-05-29 19:22:46.663][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-05-29 19:22:46.663][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-05-29 19:22:46.663][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-05-29 19:22:46.665][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:46.667][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-29 19:22:46.667][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-29 19:22:46.667][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-29 19:22:46.668][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-29 19:22:46.670][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:46.671][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:46.672][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-29 19:22:46.673][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:46.674][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:46.675][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-29 19:22:46.676][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-29 19:22:46.676][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-05-29 19:22:46.676][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-29 19:22:46.677][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-29 19:22:46.678][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:46.679][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-05-29 19:22:46.679][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-05-29 19:22:46.681][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-29 19:22:46.682][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-29 19:22:46.684][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-05-29 19:22:46.686][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-29 19:22:46.688][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-29 19:22:46.689][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-29 19:22:46.693][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-05-29 19:22:46.694][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-05-29 19:22:46.695][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-05-29 19:22:46.697][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-05-29 19:22:46.698][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-29 19:22:46.698][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-29 19:22:46.700][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-05-29 19:22:46.700][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-05-29 19:22:46.708][biodb::testThat]
biodb.INFO [2024-05-29 19:22:46.709][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-05-29 19:22:46.710][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:22:46.711][biodb::testThat]
biodb.DEBUG[2024-05-29 19:22:46.713][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-05-29 19:22:46.717][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-29 19:22:46.718][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-05-29 19:22:46.719][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-29 19:22:46.721][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-05-29 19:22:46.724][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-29 19:22:46.726][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:22:46.727][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:22:46.730][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-05-29 19:22:47.069][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-05-29 19:22:47.407][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:22:47.409][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2024-05-29 19:22:47.413][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2024-05-29 19:22:47.423][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-29 19:22:47.424][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-05-29 19:22:47.425][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-05-29 19:22:47.426][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-29 19:22:47.427][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:47.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:47.428][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:47.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:47.431][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:47.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-29 19:22:47.449][biodb::testContext]
biodb.INFO [2024-05-29 19:22:47.451][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-29 19:22:47.453][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-05-29 19:22:47.454][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-29 19:22:47.456][biodb::testContext]
biodb.INFO [2024-05-29 19:22:47.458][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-29 19:22:47.460][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-29 19:22:47.464][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-29 19:22:47.465][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-29 19:22:47.466][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-29 19:22:47.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:47.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:47.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:47.469][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-29 19:22:47.470][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-29 19:22:47.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:47.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:47.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:47.473][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-29 19:22:47.474][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-29 19:22:47.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:47.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:47.476][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.DEBUG[2024-05-29 19:22:47.477][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-29 19:22:47.478][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-29 19:22:47.479][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-29 19:22:47.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:47.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:47.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:47.483][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-29 19:22:47.483][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-29 19:22:47.484][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-29 19:22:47.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:47.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:47.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:47.487][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-29 19:22:47.488][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-29 19:22:47.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:47.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:47.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:47.492][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-29 19:22:47.493][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-29 19:22:47.494][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-29 19:22:47.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:47.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:47.496][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[2024-05-29 19:22:47.497][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-29 19:22:47.498][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-29 19:22:47.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:47.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:47.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:47.501][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-29 19:22:47.502][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-29 19:22:47.503][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-29 19:22:47.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:47.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:47.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:47.506][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-29 19:22:47.507][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-29 19:22:47.508][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-29 19:22:47.509][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-29 19:22:47.510][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-29 19:22:47.510][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-29 19:22:47.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:47.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:47.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:47.513][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-29 19:22:47.514][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-29 19:22:47.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:47.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:47.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:47.518][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-29 19:22:47.519][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-29 19:22:47.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:47.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:47.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:47.522][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-29 19:22:47.523][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-29 19:22:47.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:47.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:47.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:47.528][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-29 19:22:47.529][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-29 19:22:47.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:47.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:47.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:47.532][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-29 19:22:47.533][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-29 19:22:47.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:47.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:47.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:47.537][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-29 19:22:47.537][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-29 19:22:47.851][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-29 19:22:47.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:47.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:47.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:47.855][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-29 19:22:47.856][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-29 19:22:47.857][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-29 19:22:47.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:47.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:47.859][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[2024-05-29 19:22:47.860][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-29 19:22:47.861][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:47.862][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-29 19:22:47.864][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:47.864][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-29 19:22:47.865][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:47.866][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-29 19:22:47.867][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:47.868][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-29 19:22:47.870][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-29 19:22:47.871][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-29 19:22:47.872][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:47.874][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-29 19:22:47.875][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-29 19:22:47.875][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:47.876][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:47.877][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-29 19:22:47.877][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-29 19:22:47.877][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-29 19:22:47.877][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-29 19:22:47.877][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-29 19:22:47.879][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-29 19:22:47.880][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:47.881][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:47.881][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-29 19:22:47.882][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:47.883][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:47.895][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-29 19:22:47.897][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:47.898][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-29 19:22:47.899][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-29 19:22:47.899][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:47.901][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:47.902][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-29 19:22:47.903][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:47.904][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-29 19:22:47.905][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:47.906][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-29 19:22:47.920][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:47.921][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-29 19:22:47.923][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:47.924][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-29 19:22:47.925][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-29 19:22:47.926][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-29 19:22:47.927][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:47.928][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-29 19:22:47.929][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-29 19:22:47.930][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:47.930][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:47.931][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-29 19:22:47.931][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-29 19:22:47.931][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-29 19:22:47.931][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-29 19:22:47.931][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-29 19:22:47.932][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-29 19:22:47.933][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:47.935][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:47.936][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-29 19:22:47.937][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:47.938][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:47.939][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-29 19:22:47.939][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:47.940][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-29 19:22:47.941][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-29 19:22:47.942][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:47.943][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:47.944][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-29 19:22:47.945][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:47.947][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-29 19:22:47.947][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:47.948][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-29 19:22:47.949][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:47.950][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-29 19:22:47.951][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:47.951][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-29 19:22:47.952][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-29 19:22:47.953][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-29 19:22:47.954][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:47.955][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-29 19:22:47.955][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-29 19:22:47.956][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:47.957][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:47.959][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:47.960][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-29 19:22:47.961][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:47.961][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:47.962][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-29 19:22:47.963][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:47.964][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:47.965][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-29 19:22:47.965][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:47.966][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-29 19:22:47.967][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-29 19:22:47.968][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:47.969][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:47.970][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-29 19:22:47.985][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:47.986][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-29 19:22:47.987][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:47.988][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-29 19:22:47.989][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:47.990][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-29 19:22:47.991][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:47.991][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-29 19:22:47.992][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-29 19:22:47.993][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-29 19:22:47.994][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:47.995][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-29 19:22:48.011][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-29 19:22:48.012][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:48.013][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:48.014][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:48.015][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-29 19:22:48.016][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:48.017][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:48.017][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-29 19:22:48.018][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:48.019][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:48.020][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-29 19:22:48.022][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:48.023][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-29 19:22:48.024][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-29 19:22:48.025][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:48.026][self$setPropertyValue]
biodb.DEBUG[2024-05-29 19:22:48.027][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-29 19:22:48.028][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:48.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:48.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:48.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:48.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:48.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:48.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:48.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:48.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:48.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:48.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:48.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:48.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:48.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:48.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:48.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:48.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:48.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:48.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:48.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:48.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:48.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:48.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:48.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:48.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:48.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:48.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:48.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:48.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:48.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:48.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:48.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:48.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:48.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:48.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:48.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:48.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:48.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:48.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:48.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:48.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:48.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:48.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:48.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:48.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:48.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:48.082][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[2024-05-29 19:22:48.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:48.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:48.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:48.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:48.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:48.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:48.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:48.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:48.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:48.091][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[2024-05-29 19:22:48.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:48.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:48.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:48.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:48.104][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[2024-05-29 19:22:48.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:48.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:48.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:48.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:48.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:48.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:48.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:48.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:48.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:48.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:48.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:48.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:48.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:48.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:48.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:48.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:48.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:48.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:48.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:48.122][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[2024-05-29 19:22:48.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:48.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:48.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:48.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:48.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:48.127][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-29 19:22:48.128][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-29 19:22:48.129][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-29 19:22:48.130][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-29 19:22:48.132][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-29 19:22:48.133][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-29 19:22:48.134][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-29 19:22:48.135][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-29 19:22:48.136][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-29 19:22:48.138][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-29 19:22:48.139][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-29 19:22:48.140][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-29 19:22:48.141][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-29 19:22:48.142][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-29 19:22:48.143][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-29 19:22:48.144][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-29 19:22:48.146][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-29 19:22:48.147][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-29 19:22:48.148][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-29 19:22:48.149][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-29 19:22:48.150][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-29 19:22:48.151][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-29 19:22:48.153][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-29 19:22:48.154][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-29 19:22:48.155][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-29 19:22:48.156][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-29 19:22:48.158][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-29 19:22:48.159][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-29 19:22:48.160][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-29 19:22:48.161][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-29 19:22:48.162][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-29 19:22:48.163][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-29 19:22:48.165][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-29 19:22:48.166][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-29 19:22:48.167][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-29 19:22:48.168][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-29 19:22:48.170][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-29 19:22:48.171][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-29 19:22:48.173][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-29 19:22:48.174][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-29 19:22:48.175][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-29 19:22:48.176][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-29 19:22:48.177][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-29 19:22:48.178][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-29 19:22:48.179][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-29 19:22:48.181][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-29 19:22:48.183][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-29 19:22:48.184][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-29 19:22:48.185][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-29 19:22:48.186][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-29 19:22:48.187][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-29 19:22:48.188][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-29 19:22:48.189][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-29 19:22:48.190][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-29 19:22:48.192][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-29 19:22:48.193][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-29 19:22:48.195][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-29 19:22:48.196][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-29 19:22:48.197][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-29 19:22:48.198][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-29 19:22:48.199][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-29 19:22:48.200][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-29 19:22:48.201][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-29 19:22:48.202][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-29 19:22:48.204][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-29 19:22:48.206][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-29 19:22:48.207][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-29 19:22:48.208][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-29 19:22:48.209][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-29 19:22:48.210][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-29 19:22:48.211][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-29 19:22:48.213][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-29 19:22:48.214][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-29 19:22:48.215][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-29 19:22:48.217][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-29 19:22:48.218][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-29 19:22:48.220][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-29 19:22:48.221][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-29 19:22:48.222][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-29 19:22:48.223][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-29 19:22:48.224][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-29 19:22:48.225][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-29 19:22:48.226][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-29 19:22:48.228][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-29 19:22:48.242][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-29 19:22:48.243][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-29 19:22:48.244][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:48.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:48.245][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:48.246][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.DEBUG[2024-05-29 19:22:48.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:48.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:48.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:48.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:48.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:48.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:48.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:48.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:48.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:48.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:48.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:48.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:48.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:48.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:48.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:48.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:48.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:48.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:48.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:48.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:48.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:48.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:48.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:48.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:48.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:48.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:48.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:48.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:48.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:48.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:48.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:48.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:48.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:48.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:48.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:48.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:48.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:48.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:48.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:48.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:48.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:48.291][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[2024-05-29 19:22:48.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:48.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:48.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:48.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:48.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:48.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:48.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:48.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:48.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:48.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:48.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:48.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:48.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:48.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:48.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:48.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:48.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:48.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:48.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:48.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:48.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:48.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:48.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:48.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:48.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:48.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:48.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:48.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:48.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:48.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:48.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:48.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:48.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:48.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:48.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:48.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:48.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:48.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:48.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:48.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:48.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:48.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:48.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:48.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:48.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:48.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:48.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:48.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:48.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:48.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:48.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:48.335][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:48.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:48.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:48.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:48.338][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[2024-05-29 19:22:48.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:48.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:48.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:48.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:48.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:48.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:48.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:48.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:48.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:48.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:48.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:48.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:48.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:48.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:48.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-29 19:22:48.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:48.352][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:48.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:48.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:48.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:48.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:48.358][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-05-29 19:22:48.359][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-05-29 19:22:48.361][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:48.361][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-29 19:22:48.362][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:48.363][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-29 19:22:48.364][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:48.365][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-29 19:22:48.366][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:48.367][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-05-29 19:22:48.368][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-29 19:22:48.369][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-29 19:22:48.370][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:48.370][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-05-29 19:22:48.371][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-29 19:22:48.372][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-05-29 19:22:48.372][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-05-29 19:22:48.372][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-05-29 19:22:48.372][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-05-29 19:22:48.372][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-05-29 19:22:48.372][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-05-29 19:22:48.372][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-05-29 19:22:48.372][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-05-29 19:22:48.372][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-05-29 19:22:48.372][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-05-29 19:22:48.372][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-05-29 19:22:48.373][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-29 19:22:48.374][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-29 19:22:48.374][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-29 19:22:48.374][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-29 19:22:48.375][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-29 19:22:48.376][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:48.377][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:48.378][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-29 19:22:48.379][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-29 19:22:48.379][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-29 19:22:48.380][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-29 19:22:48.381][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-29 19:22:48.381][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-05-29 19:22:48.382][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-29 19:22:48.383][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-29 19:22:48.383][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-29 19:22:48.384][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-05-29 19:22:48.384][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-05-29 19:22:48.385][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-29 19:22:48.387][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-29 19:22:48.409][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-05-29 19:22:48.411][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-29 19:22:48.413][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-29 19:22:48.414][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-29 19:22:48.417][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-05-29 19:22:48.418][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-05-29 19:22:48.419][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-05-29 19:22:48.421][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-05-29 19:22:48.422][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-29 19:22:48.423][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-29 19:22:48.424][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-05-29 19:22:48.425][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-05-29 19:22:48.427][biodb::testThat]
biodb.INFO [2024-05-29 19:22:48.427][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-05-29 19:22:48.428][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-29 19:22:48.429][biodb::testThat]
biodb.DEBUG[2024-05-29 19:22:48.432][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-05-29 19:22:48.435][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-29 19:22:48.436][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-05-29 19:22:48.437][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-29 19:22:48.446][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-05-29 19:22:48.452][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-29 19:22:48.455][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-29 19:22:48.457][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-05-29 19:22:48.458][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-29 19:22:48.460][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-05-29 19:22:48.464][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-05-29 19:22:48.465][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-29 19:22:48.467][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-05-29 19:22:48.468][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-29 19:22:48.469][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-29 19:22:48.470][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-29 19:22:48.471][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-29 19:22:48.471][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-29 19:22:48.472][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-29 19:22:48.475][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:48.475][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:48.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:48.491][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:48.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:48.494][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:48.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-29 19:22:48.500][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2024-05-29 19:22:48.505][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-29 19:22:48.506][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-29 19:22:48.509][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2024-05-29 19:22:48.874][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2024-05-29 19:22:50.008][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-29 19:22:50.012][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2024-05-29 19:22:50.024][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2024-05-29 19:22:50.030][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2024-05-29 19:22:50.036][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-29 19:22:50.038][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-29 19:22:50.041][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-29 19:22:50.043][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-29 19:22:50.045][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:50.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:50.054][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:50.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:50.057][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:50.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-29 19:22:50.066][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:50.068][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:50.069][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:50.071][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:50.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:50.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:50.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:50.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:50.098][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:22:50.100][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:22:50.101][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:50.103][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:50.106][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-29 19:22:50.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-29 19:22:50.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:50.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:50.112][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:22:50.114][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:22:50.115][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:50.118][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:50.120][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-29 19:22:50.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-29 19:22:50.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:50.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:50.124][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-29 19:22:50.125][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-29 19:22:50.126][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:50.127][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:50.131][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-29 19:22:50.132][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-29 19:22:50.133][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:50.135][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:50.137][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:50.138][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:50.138][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:50.139][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:50.142][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:50.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-29 19:22:50.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:50.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:50.147][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:22:50.148][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:50.149][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:50.151][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:50.153][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-29 19:22:50.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-29 19:22:50.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:50.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:50.158][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:50.159][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:50.160][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:50.161][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:50.162][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:50.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-29 19:22:50.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:50.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:50.168][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:50.170][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:50.172][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:50.173][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:50.175][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-29 19:22:50.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-29 19:22:50.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:50.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:50.180][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:22:50.182][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:22:50.183][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:50.184][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:50.187][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-29 19:22:50.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-29 19:22:50.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:50.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:50.193][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:22:50.194][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:22:50.195][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:50.196][ef$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:50.198][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-29 19:22:50.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-29 19:22:50.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:50.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:50.203][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:50.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:50.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:50.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:50.209][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:50.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:50.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:50.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:50.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:50.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:50.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:50.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:50.220][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-29 19:22:50.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-29 19:22:50.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:50.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:50.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:50.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:50.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:50.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:50.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:50.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:50.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:50.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:50.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:50.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:50.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:50.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:50.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:50.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:50.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:50.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:50.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:50.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:50.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:50.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-29 19:22:50.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-29 19:22:50.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-29 19:22:50.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-29 19:22:50.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-29 19:22:50.256][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-05-29 19:22:50.262][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-29 19:22:50.264][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-05-29 19:22:50.266][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-05-29 19:22:50.267][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-29 19:22:50.268][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-29 19:22:50.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-29 19:22:50.270][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-29 19:22:50.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-29 19:22:50.273][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-29 19:22:50.274][FUN] Functions in observer 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 
 24.344   1.658  74.843

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

nameusersystemelapsed
ChebiConn2.6620.9934.899
ChebiEntry0.4740.0270.521